diff --git a/modules/build/src/main/scala/scala/build/Build.scala b/modules/build/src/main/scala/scala/build/Build.scala
index 79b1c0a69c..39db8ac0f2 100644
--- a/modules/build/src/main/scala/scala/build/Build.scala
+++ b/modules/build/src/main/scala/scala/build/Build.scala
@@ -233,7 +233,8 @@ object Build {
           () => options.javaHome().value.javaCommand
         ),
         logger,
-        options.suppressWarningOptions
+        options.suppressWarningOptions,
+        options.internal.exclude
       )
     }
     val sharedOptions = crossSources.sharedOptions(options)
diff --git a/modules/build/src/main/scala/scala/build/CrossSources.scala b/modules/build/src/main/scala/scala/build/CrossSources.scala
index f2a54ca24c..c3777ffc47 100644
--- a/modules/build/src/main/scala/scala/build/CrossSources.scala
+++ b/modules/build/src/main/scala/scala/build/CrossSources.scala
@@ -1,12 +1,20 @@
 package scala.build
 
+import java.io.File
+
 import scala.build.EitherCps.{either, value}
 import scala.build.Ops.*
 import scala.build.Positioned
-import scala.build.errors.{BuildException, CompositeBuildException, MalformedDirectiveError}
+import scala.build.errors.{
+  BuildException,
+  CompositeBuildException,
+  ExcludeDefinitionError,
+  MalformedDirectiveError
+}
 import scala.build.input.ElementsUtils.*
 import scala.build.input.*
 import scala.build.internal.Constants
+import scala.build.internal.util.RegexUtils
 import scala.build.options.{
   BuildOptions,
   BuildRequirements,
@@ -16,6 +24,9 @@ import scala.build.options.{
   WithBuildRequirements
 }
 import scala.build.preprocessing.*
+import scala.build.testrunner.DynamicTestRunner.globPattern
+import scala.util.Try
+import scala.util.chaining.*
 
 final case class CrossSources(
   paths: Seq[WithBuildRequirements[(os.Path, os.RelPath)]],
@@ -128,6 +139,7 @@ object CrossSources {
     preprocessors: Seq[Preprocessor],
     logger: Logger,
     suppressWarningOptions: SuppressWarningOptions,
+    exclude: Seq[Positioned[String]] = Nil,
     maybeRecoverOnError: BuildException => Option[BuildException] = e => Some(e)
   ): Either[BuildException, (CrossSources, Inputs)] = either {
 
@@ -155,8 +167,21 @@ object CrossSources {
         .left.map(CompositeBuildException(_))
         .map(_.flatten)
 
+    val flattenedInputs = inputs.flattened()
+    val allExclude = { // supports only one exclude directive in one source file, which should be the project file.
+      val projectScalaFileOpt = flattenedInputs.collectFirst {
+        case f: ProjectScalaFile => f
+      }
+      val excludeFromProjectFile =
+        value(preprocessSources(projectScalaFileOpt.toSeq))
+          .flatMap(_.options).flatMap(_.internal.exclude)
+      exclude ++ excludeFromProjectFile
+    }
+
     val preprocessedInputFromArgs: Seq[PreprocessedSource] =
-      value(preprocessSources(inputs.flattened()))
+      value(
+        preprocessSources(value(excludeSources(flattenedInputs, inputs.workspace, allExclude)))
+      )
 
     val sourcesFromDirectives =
       preprocessedInputFromArgs
@@ -166,11 +191,16 @@ object CrossSources {
     val inputsElemFromDirectives: Seq[SingleFile] =
       value(resolveInputsFromSources(sourcesFromDirectives, inputs.enableMarkdown))
     val preprocessedSourcesFromDirectives: Seq[PreprocessedSource] =
-      value(preprocessSources(inputsElemFromDirectives))
-    val allInputs = inputs.add(inputsElemFromDirectives)
+      value(preprocessSources(inputsElemFromDirectives.pipe(elements =>
+        value(excludeSources(elements, inputs.workspace, allExclude))
+      )))
+    val allInputs = inputs.add(inputsElemFromDirectives).filter(elems =>
+      value(excludeSources(elems, inputs.workspace, allExclude))
+    )
 
     val preprocessedSources =
       (preprocessedInputFromArgs ++ preprocessedSourcesFromDirectives).distinct
+        .pipe(sources => value(validateExcludeDirectives(sources, allInputs.workspace)))
 
     val scopedRequirements       = preprocessedSources.flatMap(_.scopedRequirements)
     val scopedRequirementsByRoot = scopedRequirements.groupBy(_.path.root)
@@ -305,4 +335,56 @@ object CrossSources {
       .left.map(CompositeBuildException(_))
       .map(_.flatten)
 
+  /** Filters out the sources from the input sequence based on the provided 'exclude' patterns. The
+    * exclude patterns can be absolute paths, relative paths, or glob patterns.
+    *
+    * @throws BuildException
+    *   If multiple 'exclude' patterns are defined across the input sources.
+    */
+  private def excludeSources[E <: Element](
+    elements: Seq[E],
+    workspaceDir: os.Path,
+    exclude: Seq[Positioned[String]]
+  ): Either[BuildException, Seq[E]] = either {
+    val excludePatterns = exclude.map(_.value).flatMap { p =>
+      val maybeRelPath = Try(os.RelPath(p)).toOption
+      maybeRelPath match {
+        case Some(relPath) if os.isDir(workspaceDir / relPath) =>
+          // exclude relative directory paths, add * to exclude all files in the directory
+          Seq(p, (workspaceDir / relPath / "*").toString)
+        case Some(relPath) =>
+          Seq(p, (workspaceDir / relPath).toString) // exclude relative paths
+        case None => Seq(p)
+      }
+    }
+
+    def isSourceIncluded(path: String, excludePatterns: Seq[String]): Boolean =
+      excludePatterns
+        .forall(pattern => !RegexUtils.globPattern(pattern).matcher(path).matches())
+
+    elements.filter {
+      case e: OnDisk => isSourceIncluded(e.path.toString, excludePatterns)
+      case _         => true
+    }
+  }
+
+  /** Validates that exclude directives are defined only in the one source.
+    */
+  def validateExcludeDirectives(
+    sources: Seq[PreprocessedSource],
+    workspaceDir: os.Path
+  ): Either[BuildException, Seq[PreprocessedSource]] = {
+    val excludeDirectives = sources.flatMap(_.options).map(_.internal.exclude).toList.flatten
+
+    excludeDirectives match {
+      case Nil | Seq(_) =>
+        Right(sources)
+      case _ =>
+        val expectedProjectFilePath = workspaceDir / Constants.projectFileName
+        Left(new ExcludeDefinitionError(
+          excludeDirectives.flatMap(_.positions),
+          expectedProjectFilePath
+        ))
+    }
+  }
 }
diff --git a/modules/build/src/main/scala/scala/build/bsp/BspImpl.scala b/modules/build/src/main/scala/scala/build/bsp/BspImpl.scala
index f94e15c569..1aa8a73251 100644
--- a/modules/build/src/main/scala/scala/build/bsp/BspImpl.scala
+++ b/modules/build/src/main/scala/scala/build/bsp/BspImpl.scala
@@ -108,6 +108,7 @@ final class BspImpl(
         ),
         logger = persistentLogger,
         suppressWarningOptions = buildOptions.suppressWarningOptions,
+        exclude = buildOptions.internal.exclude,
         maybeRecoverOnError = maybeRecoverOnError(Scope.Main)
       ).left.map((_, Scope.Main))
     }
diff --git a/modules/build/src/main/scala/scala/build/input/Inputs.scala b/modules/build/src/main/scala/scala/build/input/Inputs.scala
index 113213b2f2..331ee51981 100644
--- a/modules/build/src/main/scala/scala/build/input/Inputs.scala
+++ b/modules/build/src/main/scala/scala/build/input/Inputs.scala
@@ -65,6 +65,8 @@ final case class Inputs(
 
   def add(extraElements: Seq[Element]): Inputs =
     if elements.isEmpty then this else copy(elements = (elements ++ extraElements).distinct)
+  def filter(filterElements: Seq[Element] => Seq[Element]): Inputs =
+    copy(elements = filterElements(elements))
 
   def generatedSrcRoot(scope: Scope): os.Path =
     workspace / Constants.workspaceDirName / projectName / "src_generated" / scope.name
diff --git a/modules/build/src/main/scala/scala/build/internal/util/RegexUtils.scala b/modules/build/src/main/scala/scala/build/internal/util/RegexUtils.scala
new file mode 100644
index 0000000000..c4c5abc061
--- /dev/null
+++ b/modules/build/src/main/scala/scala/build/internal/util/RegexUtils.scala
@@ -0,0 +1,23 @@
+package scala.build.internal.util
+
+import java.util.regex.Pattern
+
+object RegexUtils {
+
+  /** Based on junit-interface [GlobFilter.
+    * compileGlobPattern](https://github.com/sbt/junit-interface/blob/f8c6372ed01ce86f15393b890323d96afbe6d594/src/main/java/com/novocode/junit/GlobFilter.java#L37)
+    *
+    * @return
+    *   Pattern allows to regex input which contains only *, for example `*foo*` match to
+    *   `MyTests.foo`
+    */
+  def globPattern(expr: String): Pattern = {
+    val a = expr.split("\\*", -1)
+    val b = new StringBuilder()
+    for (i <- 0 until a.length) {
+      if (i != 0) b.append(".*")
+      if (a(i).nonEmpty) b.append(Pattern.quote(a(i).replaceAll("\n", "\\n")))
+    }
+    Pattern.compile(b.toString)
+  }
+}
diff --git a/modules/build/src/main/scala/scala/build/preprocessing/ScalaPreprocessor.scala b/modules/build/src/main/scala/scala/build/preprocessing/ScalaPreprocessor.scala
index a09f003a07..74a8994ca4 100644
--- a/modules/build/src/main/scala/scala/build/preprocessing/ScalaPreprocessor.scala
+++ b/modules/build/src/main/scala/scala/build/preprocessing/ScalaPreprocessor.scala
@@ -67,6 +67,7 @@ case object ScalaPreprocessor extends Preprocessor {
 
   val usingDirectiveHandlers: Seq[DirectiveHandler[BuildOptions]] =
     Seq[DirectiveHandler[_ <: HasBuildOptions]](
+      directives.Exclude.handler,
       directives.JavaHome.handler,
       directives.Jvm.handler,
       directives.MainClass.handler,
diff --git a/modules/build/src/test/scala/scala/build/tests/ExcludeTests.scala b/modules/build/src/test/scala/scala/build/tests/ExcludeTests.scala
new file mode 100644
index 0000000000..7d42e5f63a
--- /dev/null
+++ b/modules/build/src/test/scala/scala/build/tests/ExcludeTests.scala
@@ -0,0 +1,183 @@
+package scala.build.tests
+
+import com.eed3si9n.expecty.Expecty.expect
+import coursier.cache.{ArchiveCache, Cache}
+import coursier.util.{Artifact, Task}
+
+import java.io.File
+import scala.build.Ops.*
+import scala.build.Sources
+import scala.build.internal.CustomCodeWrapper
+import scala.build.CrossSources
+import scala.build.errors.ExcludeDefinitionError
+import scala.build.options.{BuildOptions, Scope, SuppressWarningOptions}
+
+class ExcludeTests extends munit.FunSuite {
+
+  val preprocessors = Sources.defaultPreprocessors(
+    CustomCodeWrapper,
+    ArchiveCache().withCache(
+      new Cache[Task] {
+        def fetch = _ => sys.error("shouldn't be used")
+
+        def file(artifact: Artifact) = sys.error("shouldn't be used")
+
+        def ec = sys.error("shouldn't be used")
+      }
+    ),
+    None,
+    () => sys.error("shouldn't be used")
+  )
+
+  test("throw error when exclude found in multiple file") {
+    val testInputs = TestInputs(
+      os.rel / "Hello.scala" ->
+        """//> using exclude "*.sc"
+          |""".stripMargin,
+      os.rel / "Main.scala" ->
+        """//> using exclude "*/test/*"
+          |""".stripMargin
+    )
+    testInputs.withInputs { (_, inputs) =>
+      val crossSources =
+        CrossSources.forInputs(
+          inputs,
+          preprocessors,
+          TestLogger(),
+          SuppressWarningOptions()
+        )
+      crossSources match {
+        case Left(_: ExcludeDefinitionError) =>
+        case o                               => fail("Exception expected", clues(o))
+      }
+    }
+  }
+
+  test("throw error when exclude found in non top-level project.scala and file") {
+    val testInputs = TestInputs(
+      os.rel / "Main.scala" ->
+        """//> using exclude "*/test/*"
+          |""".stripMargin,
+      os.rel / "src" / "project.scala" ->
+        s"""//> using exclude "*.sc" """
+    )
+    testInputs.withInputs { (_, inputs) =>
+      val crossSources =
+        CrossSources.forInputs(
+          inputs,
+          preprocessors,
+          TestLogger(),
+          SuppressWarningOptions()
+        )
+      crossSources match {
+        case Left(_: ExcludeDefinitionError) =>
+        case o                               => fail("Exception expected", clues(o))
+      }
+    }
+  }
+
+  test("exclude relative paths") {
+    val testInputs = TestInputs(
+      os.rel / "Hello.scala" -> "object Hello",
+      os.rel / "Main.scala" ->
+        """object Main {
+          |}""".stripMargin,
+      os.rel / "project.scala" ->
+        s"""//> using exclude "Main.scala" """
+    )
+    testInputs.withInputs { (_, inputs) =>
+      val (crossSources, _) =
+        CrossSources.forInputs(
+          inputs,
+          preprocessors,
+          TestLogger(),
+          SuppressWarningOptions()
+        ).orThrow
+      val scopedSources = crossSources.scopedSources(BuildOptions()).orThrow
+      val sources = scopedSources.sources(Scope.Main, crossSources.sharedOptions(BuildOptions()))
+
+      expect(sources.paths.nonEmpty)
+      expect(sources.paths.length == 2)
+      expect(sources.paths.map(_._2) == Seq(os.rel / "Hello.scala", os.rel / "project.scala"))
+    }
+  }
+
+  test("exclude absolute file paths") {
+    val testInputs = TestInputs(
+      os.rel / "Hello.scala" -> "object Hello",
+      os.rel / "Main.scala" ->
+        """object Main {
+          |}""".stripMargin,
+      os.rel / "project.scala" ->
+        s"""//> using exclude "$${.}${File.separator}Main.scala" """
+    )
+    testInputs.withInputs { (_, inputs) =>
+      val (crossSources, _) =
+        CrossSources.forInputs(
+          inputs,
+          preprocessors,
+          TestLogger(),
+          SuppressWarningOptions()
+        ).orThrow
+      val scopedSources = crossSources.scopedSources(BuildOptions()).orThrow
+      val sources = scopedSources.sources(Scope.Main, crossSources.sharedOptions(BuildOptions()))
+
+      expect(sources.paths.nonEmpty)
+      expect(sources.paths.length == 2)
+      expect(sources.paths.map(_._2) == Seq(os.rel / "Hello.scala", os.rel / "project.scala"))
+    }
+  }
+
+  test("exclude relative directory paths") {
+    val testInputs = TestInputs(
+      os.rel / "Hello.scala" -> "object Hello",
+      os.rel / "src" / "scala" / "Main.scala" ->
+        """object Main {
+          |}""".stripMargin,
+      os.rel / "project.scala" ->
+        """//> using exclude "src/*.scala" """
+    )
+    testInputs.withInputs { (_, inputs) =>
+      val (crossSources, _) =
+        CrossSources.forInputs(
+          inputs,
+          preprocessors,
+          TestLogger(),
+          SuppressWarningOptions()
+        ).orThrow
+      val scopedSources = crossSources.scopedSources(BuildOptions()).orThrow
+      val sources = scopedSources.sources(Scope.Main, crossSources.sharedOptions(BuildOptions()))
+
+      expect(sources.paths.nonEmpty)
+      expect(sources.paths.length == 2)
+      expect(sources.paths.map(_._2) == Seq(os.rel / "Hello.scala", os.rel / "project.scala"))
+    }
+  }
+
+  test("exclude relative directory paths with glob pattern") {
+    val testInputs = TestInputs(
+      os.rel / "Hello.scala" -> "object Hello",
+      os.rel / "src" / "scala" / "Main.scala" ->
+        """object Main {
+          |}""".stripMargin,
+      os.rel / "project.scala" ->
+        """//> using exclude "src/*.scala" """
+    )
+    testInputs.withInputs { (_, inputs) =>
+      val (crossSources, _) =
+        CrossSources.forInputs(
+          inputs,
+          preprocessors,
+          TestLogger(),
+          SuppressWarningOptions()
+        ).orThrow
+      val scopedSources = crossSources.scopedSources(BuildOptions()).orThrow
+      val sources = scopedSources.sources(Scope.Main, crossSources.sharedOptions(BuildOptions()))
+
+      expect(sources.paths.nonEmpty)
+      expect(sources.paths.length == 2)
+      expect(sources.paths.map(_._2) == Seq(os.rel / "Hello.scala", os.rel / "project.scala"))
+    }
+  }
+
+}
diff --git a/modules/cli/src/main/scala/scala/cli/commands/bsp/Bsp.scala b/modules/cli/src/main/scala/scala/cli/commands/bsp/Bsp.scala
index d45f247d89..e44d8e10fe 100644
--- a/modules/cli/src/main/scala/scala/cli/commands/bsp/Bsp.scala
+++ b/modules/cli/src/main/scala/scala/cli/commands/bsp/Bsp.scala
@@ -59,7 +59,8 @@ object Bsp extends ScalaCommand[BspOptions] {
                 () => buildOptions0.javaHome().value.javaCommand
               ),
               persistentLogger,
-              buildOptions0.suppressWarningOptions
+              buildOptions0.suppressWarningOptions,
+              buildOptions0.internal.exclude
             ).map(_._2).getOrElse(initialInputs)
 
           Build.updateInputs(allInputs, buildOptions(sharedOptions))
diff --git a/modules/cli/src/main/scala/scala/cli/commands/dependencyupdate/DependencyUpdate.scala b/modules/cli/src/main/scala/scala/cli/commands/dependencyupdate/DependencyUpdate.scala
index 5d1534e7f0..b5cc33410b 100644
--- a/modules/cli/src/main/scala/scala/cli/commands/dependencyupdate/DependencyUpdate.scala
+++ b/modules/cli/src/main/scala/scala/cli/commands/dependencyupdate/DependencyUpdate.scala
@@ -40,7 +40,8 @@ object DependencyUpdate extends ScalaCommand[DependencyUpdateOptions] {
           () => buildOptions.javaHome().value.javaCommand
         ),
         logger,
-        buildOptions.suppressWarningOptions
+        buildOptions.suppressWarningOptions,
+        buildOptions.internal.exclude
       ).orExit(logger)
 
     val scopedSources = crossSources.scopedSources(buildOptions).orExit(logger)
diff --git a/modules/cli/src/main/scala/scala/cli/commands/export0/Export.scala b/modules/cli/src/main/scala/scala/cli/commands/export0/Export.scala
index 55c8f6a0ea..ebb3e1d69e 100644
--- a/modules/cli/src/main/scala/scala/cli/commands/export0/Export.scala
+++ b/modules/cli/src/main/scala/scala/cli/commands/export0/Export.scala
@@ -50,7 +50,8 @@ object Export extends ScalaCommand[ExportOptions] {
           () => buildOptions.javaHome().value.javaCommand
         ),
         logger,
-        buildOptions.suppressWarningOptions
+        buildOptions.suppressWarningOptions,
+        buildOptions.internal.exclude
       )
     }
     val scopedSources = value(crossSources.scopedSources(buildOptions))
diff --git a/modules/cli/src/main/scala/scala/cli/commands/publish/PublishSetup.scala b/modules/cli/src/main/scala/scala/cli/commands/publish/PublishSetup.scala
index 1b5389dae9..fbebaf4719 100644
--- a/modules/cli/src/main/scala/scala/cli/commands/publish/PublishSetup.scala
+++ b/modules/cli/src/main/scala/scala/cli/commands/publish/PublishSetup.scala
@@ -90,7 +90,8 @@ object PublishSetup extends ScalaCommand[PublishSetupOptions] {
           () => cliBuildOptions.javaHome().value.javaCommand
         ),
         logger,
-        cliBuildOptions.suppressWarningOptions
+        cliBuildOptions.suppressWarningOptions,
+        cliBuildOptions.internal.exclude
       ).orExit(logger)
 
       val crossSourcesSharedOptions = crossSources.sharedOptions(cliBuildOptions)
diff --git a/modules/cli/src/main/scala/scala/cli/commands/setupide/SetupIde.scala b/modules/cli/src/main/scala/scala/cli/commands/setupide/SetupIde.scala
index 5b0e896787..8ba3f49f7b 100644
--- a/modules/cli/src/main/scala/scala/cli/commands/setupide/SetupIde.scala
+++ b/modules/cli/src/main/scala/scala/cli/commands/setupide/SetupIde.scala
@@ -40,7 +40,8 @@ object SetupIde extends ScalaCommand[SetupIdeOptions] {
             () => options.javaHome().value.javaCommand
           ),
           logger,
-          options.suppressWarningOptions
+          options.suppressWarningOptions,
+          options.internal.exclude
         )
       }
 
diff --git a/modules/cli/src/main/scala/scala/cli/commands/shared/SharedOptions.scala b/modules/cli/src/main/scala/scala/cli/commands/shared/SharedOptions.scala
index d81d43d74f..72d92eab00 100644
--- a/modules/cli/src/main/scala/scala/cli/commands/shared/SharedOptions.scala
+++ b/modules/cli/src/main/scala/scala/cli/commands/shared/SharedOptions.scala
@@ -203,7 +203,9 @@ final case class SharedOptions(
   @Name("toolkit")
   @Tag(tags.implementation)
   @Tag(tags.inShortHelp)
-    withToolkit: Option[String] = None
+    withToolkit: Option[String] = None,
+  @HelpMessage("Exclude sources")
+    exclude: List[String] = Nil,
 ) extends HasGlobalOptions {
   // format: on
 
@@ -363,7 +365,8 @@ final case class SharedOptions(
         localRepository = LocalRepo.localRepo(Directories.directories.localRepoDir),
         verbosity = Some(logging.verbosity),
         strictBloopJsonCheck = strictBloopJsonCheck,
-        interactive = Some(() => interactive)
+        interactive = Some(() => interactive),
+        exclude = exclude.map(Positioned.commandLine)
       ),
       notForBloopOptions = bo.PostBuildOptions(
         scalaJsLinkerOptions = linkerOptions(js),
diff --git a/modules/core/src/main/scala/scala/build/errors/ExcludeDefinitionError.scala b/modules/core/src/main/scala/scala/build/errors/ExcludeDefinitionError.scala
new file mode 100644
index 0000000000..20fc2a2351
--- /dev/null
+++ b/modules/core/src/main/scala/scala/build/errors/ExcludeDefinitionError.scala
@@ -0,0 +1,10 @@
+package scala.build.errors
+
+import scala.build.Position
+
+final class ExcludeDefinitionError(positions: Seq[Position], expectedProjectFilePath: os.Path)
+    extends BuildException(
+      s"""Found exclude directives in files:
+         |  ${positions.map(_.render()).distinct.mkString(", ")}
+         |exclude directive must be defined in project configuration file: $expectedProjectFilePath.""".stripMargin
+    )
diff --git a/modules/directives/src/main/scala/scala/build/preprocessing/directives/Exclude.scala b/modules/directives/src/main/scala/scala/build/preprocessing/directives/Exclude.scala
new file mode 100644
index 0000000000..8293f331ce
--- /dev/null
+++ b/modules/directives/src/main/scala/scala/build/preprocessing/directives/Exclude.scala
@@ -0,0 +1,38 @@
+package scala.build.preprocessing.directives
+
+import scala.build.EitherCps.{either, value}
+import scala.build.Ops.*
+import scala.build.directives.*
+import scala.build.errors.{BuildException, CompositeBuildException, WrongSourcePathError}
+import scala.build.options.{BuildOptions, InternalOptions, JavaOpt, ShadowingSeq}
+import scala.build.{Logger, Positioned, options}
+import scala.cli.commands.SpecificationLevel
+import scala.util.Try
+
+@DirectiveGroupName("Exclude sources")
+@DirectiveExamples("//> using exclude \"utils.scala\"")
+@DirectiveUsage(
+  "`//> using exclude `_pattern_ | `//> using exclude `_pattern_, _pattern_ …",
+  """`//> using exclude "*.sc"`
+    |
+    |`//> using exclude "examples/*", "*/resources/*" …`""".stripMargin
+)
+@DirectiveDescription("Exclude sources from the project")
+@DirectiveLevel(SpecificationLevel.SHOULD)
+// format: off
+final case class Exclude(
+  exclude: List[Positioned[String]] = Nil                       
+) extends HasBuildOptions {
+// format: on
+  def buildOptions: Either[BuildException, BuildOptions] = either {
+    BuildOptions(
+      internal = InternalOptions(
+        exclude = exclude
+      )
+    )
+  }
+}
+
+object Exclude {
+  val handler: DirectiveHandler[Exclude] = DirectiveHandler.derive
+}
diff --git a/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala b/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala
index f9846f61e5..a2588f780b 100644
--- a/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala
+++ b/modules/integration/src/test/scala/scala/cli/integration/RunTestDefinitions.scala
@@ -1327,4 +1327,23 @@ abstract class RunTestDefinitions(val scalaVersionOpt: Option[String])
       expect(res3.out.trim().contains(s"$expectedMessage1$expectedMessage2"))
     }
   }
+  test("exclude file") {
+    val message = "Hello"
+    val inputs = TestInputs(
+      os.rel / "Hello.scala" ->
+        s"""object Hello extends App {
+           | println("$message")
+           |}""".stripMargin,
+      os.rel / "Main.scala" ->
+        """object Main {
+          | val msg: String = 1 // compilation fails
+          |}""".stripMargin
+    )
+    inputs.fromRoot { root =>
+      val res =
+        os.proc(TestUtil.cli, extraOptions, ".", "--exclude", "*Main.scala").call(cwd = root)
+      val output = res.out.trim()
+      expect(output == message)
+    }
+  }
 }
diff --git a/modules/options/src/main/scala/scala/build/options/InternalOptions.scala b/modules/options/src/main/scala/scala/build/options/InternalOptions.scala
index feb66a7f3b..f8efed0482 100644
--- a/modules/options/src/main/scala/scala/build/options/InternalOptions.scala
+++ b/modules/options/src/main/scala/scala/build/options/InternalOptions.scala
@@ -24,7 +24,8 @@ final case class InternalOptions(
     * really needed.
     */
   keepResolution: Boolean = false,
-  extraSourceFiles: Seq[Positioned[os.Path]] = Nil
+  extraSourceFiles: Seq[Positioned[os.Path]] = Nil,
+  exclude: Seq[Positioned[String]] = Nil
 ) {
   def verbosityOrDefault: Int = verbosity.getOrElse(0)
   def strictBloopJsonCheckOrDefault: Boolean =
diff --git a/website/docs/commands/compile.md b/website/docs/commands/compile.md
index 63e0d606cd..491e765a2d 100644
--- a/website/docs/commands/compile.md
+++ b/website/docs/commands/compile.md
@@ -461,3 +461,25 @@ You can also add javac options with the using directive `//> using javacOpt`:
 ```scala compile
 //> using javacOpt "source", "1.8", "target", "1.8"
 ```
+
+## Exclude sources
+
+To exclude specific source files or entire directories from a Scala CLI project, use the `exclude` directive or command
+line parameter `--exclude` along with a pattern:
+
+- an absolute path: `/root/path/to/your/project/Main.scala`
+- a relative path: `src/main/scala/Main.scala`
+- a glob pattern: `*.sc`
+
+:::note
+The `exclude` directive should be placed in your `project.scala` file, which Scala CLI uses to determine the project
+root directory.
+For more details on `project.file`, see [the `Project root directory` reference](/docs/reference/root-dir).
+:::
+
+For example, to exclude all files in the `example/scala` directory, add the following directive to your
+ `project.file` file:
+
+```scala title=project.scala
+//> using exclude "example/scala"
+```
\ No newline at end of file
diff --git a/website/docs/reference/cli-options.md b/website/docs/reference/cli-options.md
index baa1a5b16b..06d2cd1fc5 100644
--- a/website/docs/reference/cli-options.md
+++ b/website/docs/reference/cli-options.md
@@ -1497,6 +1497,10 @@ Aliases: `--toolkit`
 
 Add toolkit to classPath
 
+### `--exclude`
+
+Exclude sources
+
 ## Snippet options
 
 Available in commands:
diff --git a/website/docs/reference/directives.md b/website/docs/reference/directives.md
index 711ae15147..509ae4d218 100644
--- a/website/docs/reference/directives.md
+++ b/website/docs/reference/directives.md
@@ -68,6 +68,17 @@ Add dependencies
 
 `//> using dep "tabby:tabby:0.2.3,url=https://github.com/bjornregnell/tabby/releases/download/v0.2.3/tabby_3-0.2.3.jar"`
 
+### Exclude sources
+
+Exclude sources from the project
+
+`//> using exclude "*.sc"`
+
+`//> using exclude "examples/*", "*/resources/*" …`
+
+#### Examples
+`//> using exclude "utils.scala"`
+
 ### JVM version
 
 Use a specific JVM, such as `14`, `adopt:11`, or `graalvm:21`, or `system`
diff --git a/website/docs/reference/scala-command/cli-options.md b/website/docs/reference/scala-command/cli-options.md
index 7926be7491..43ae19391d 100644
--- a/website/docs/reference/scala-command/cli-options.md
+++ b/website/docs/reference/scala-command/cli-options.md
@@ -1008,6 +1008,12 @@ Aliases: `--toolkit`
 
 Add toolkit to classPath
 
+### `--exclude`
+
+`IMPLEMENTATION specific` per Scala Runner specification
+
+Exclude sources
+
 ## Snippet options
 
 Available in commands:
diff --git a/website/docs/reference/scala-command/directives.md b/website/docs/reference/scala-command/directives.md
index 49131d76c6..34428cec45 100644
--- a/website/docs/reference/scala-command/directives.md
+++ b/website/docs/reference/scala-command/directives.md
@@ -123,6 +123,17 @@ Manually add sources to the project
 #### Examples
 `//> using file "utils.scala"`
 
+### Exclude sources
+
+Exclude sources from the project
+
+`//> using exclude "*.sc"`
+
+`//> using exclude "examples/*", "*/resources/*" …`
+
+#### Examples
+`//> using exclude "utils.scala"`
+
 ### JVM version
 
 Use a specific JVM, such as `14`, `adopt:11`, or `graalvm:21`, or `system`
diff --git a/website/docs/reference/scala-command/runner-specification.md b/website/docs/reference/scala-command/runner-specification.md
index 03b27f3ca1..16a7ce6d94 100644
--- a/website/docs/reference/scala-command/runner-specification.md
+++ b/website/docs/reference/scala-command/runner-specification.md
@@ -572,6 +572,10 @@ Add toolkit to classPath
 
 Aliases: `--toolkit`
 
+**--exclude**
+
+Exclude sources
+
 </details>
 
 ---
@@ -1266,6 +1270,10 @@ Add toolkit to classPath
 
 Aliases: `--toolkit`
 
+**--exclude**
+
+Exclude sources
+
 </details>
 
 ---
@@ -1799,6 +1807,10 @@ Add toolkit to classPath
 
 Aliases: `--toolkit`
 
+**--exclude**
+
+Exclude sources
+
 **--java-prop-option**
 
 Add java properties. Note that options equal `-Dproperty=value` are assumed to be java properties and don't require to be passed after `--java-prop`.
@@ -2362,6 +2374,10 @@ Add toolkit to classPath
 
 Aliases: `--toolkit`
 
+**--exclude**
+
+Exclude sources
+
 **--java-prop-option**
 
 Add java properties. Note that options equal `-Dproperty=value` are assumed to be java properties and don't require to be passed after `--java-prop`.
@@ -2934,6 +2950,10 @@ Add toolkit to classPath
 
 Aliases: `--toolkit`
 
+**--exclude**
+
+Exclude sources
+
 **--java-prop-option**
 
 Add java properties. Note that options equal `-Dproperty=value` are assumed to be java properties and don't require to be passed after `--java-prop`.
@@ -3464,6 +3484,10 @@ Add toolkit to classPath
 
 Aliases: `--toolkit`
 
+**--exclude**
+
+Exclude sources
+
 **--respect-project-filters**
 
 Use project filters defined in the configuration. Turned on by default, use `--respect-project-filters:false` to disable it.
@@ -4069,6 +4093,10 @@ Add toolkit to classPath
 
 Aliases: `--toolkit`
 
+**--exclude**
+
+Exclude sources
+
 **--java-prop-option**
 
 Add java properties. Note that options equal `-Dproperty=value` are assumed to be java properties and don't require to be passed after `--java-prop`.
@@ -4675,6 +4703,10 @@ Add toolkit to classPath
 
 Aliases: `--toolkit`
 
+**--exclude**
+
+Exclude sources
+
 **--json-options**
 
 Command-line options JSON file
@@ -5518,6 +5550,10 @@ Add toolkit to classPath
 
 Aliases: `--toolkit`
 
+**--exclude**
+
+Exclude sources
+
 **--bsp-directory**
 
 Custom BSP configuration location