diff --git a/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagic.json b/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagic.json
new file mode 100644
index 0000000000000..5cb72064ec1c0
--- /dev/null
+++ b/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagic.json
@@ -0,0 +1,8 @@
+{
+  "execution_count": null,
+  "cell_type": "code",
+  "id": "1",
+  "metadata": {},
+  "outputs": [],
+  "source": ["pip install requests"]
+}
diff --git a/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagic_after_code.json b/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagic_after_code.json
new file mode 100644
index 0000000000000..619a4f7125e4e
--- /dev/null
+++ b/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagic_after_code.json
@@ -0,0 +1,8 @@
+{
+  "execution_count": null,
+  "cell_type": "code",
+  "id": "1",
+  "metadata": {},
+  "outputs": [],
+  "source": ["x = 1\n", "pip install requests"]
+}
diff --git a/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagic_before_code.json b/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagic_before_code.json
new file mode 100644
index 0000000000000..10255fca0e9b3
--- /dev/null
+++ b/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagic_before_code.json
@@ -0,0 +1,8 @@
+{
+  "execution_count": null,
+  "cell_type": "code",
+  "id": "1",
+  "metadata": {},
+  "outputs": [],
+  "source": ["pip install requests\n", "x = 1"]
+}
diff --git a/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagics.json b/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagics.json
new file mode 100644
index 0000000000000..8bd20103af602
--- /dev/null
+++ b/crates/ruff_notebook/resources/test/fixtures/jupyter/cell/automagics.json
@@ -0,0 +1,8 @@
+{
+  "execution_count": null,
+  "cell_type": "code",
+  "id": "1",
+  "metadata": {},
+  "outputs": [],
+  "source": ["pip install requests\n", "pip install requests"]
+}
diff --git a/crates/ruff_notebook/src/notebook.rs b/crates/ruff_notebook/src/notebook.rs
index 611b90cbee2e1..61994e7702648 100644
--- a/crates/ruff_notebook/src/notebook.rs
+++ b/crates/ruff_notebook/src/notebook.rs
@@ -80,13 +80,125 @@ impl Cell {
         // Ignore cells containing cell magic as they act on the entire cell
         // as compared to line magic which acts on a single line.
         !match source {
-            SourceValue::String(string) => string
-                .lines()
-                .any(|line| line.trim_start().starts_with("%%")),
-            SourceValue::StringArray(string_array) => string_array
-                .iter()
-                .any(|line| line.trim_start().starts_with("%%")),
+            SourceValue::String(string) => Self::is_magic_cell(string.lines()),
+            SourceValue::StringArray(string_array) => {
+                Self::is_magic_cell(string_array.iter().map(String::as_str))
+            }
+        }
+    }
+
+    /// Returns `true` if a cell should be ignored due to the use of cell magics.
+    fn is_magic_cell<'a>(lines: impl Iterator<Item = &'a str>) -> bool {
+        let mut lines = lines.peekable();
+
+        // Detect automatic line magics (automagic), which aren't supported by the parser. If a line
+        // magic uses automagic, Jupyter doesn't allow following it with non-magic lines anyway, so
+        // we aren't missing out on any valid Python code.
+        //
+        // For example, this is valid:
+        // ```jupyter
+        // cat /path/to/file
+        // cat /path/to/file
+        // ```
+        //
+        // But this is invalid:
+        // ```jupyter
+        // cat /path/to/file
+        // x = 1
+        // ```
+        //
+        // See: https://ipython.readthedocs.io/en/stable/interactive/magics.html
+        if lines
+            .peek()
+            .and_then(|line| line.split_whitespace().next())
+            .is_some_and(|token| {
+                matches!(
+                    token,
+                    "alias"
+                        | "alias_magic"
+                        | "autoawait"
+                        | "autocall"
+                        | "automagic"
+                        | "bookmark"
+                        | "cd"
+                        | "code_wrap"
+                        | "colors"
+                        | "conda"
+                        | "config"
+                        | "debug"
+                        | "dhist"
+                        | "dirs"
+                        | "doctest_mode"
+                        | "edit"
+                        | "env"
+                        | "gui"
+                        | "history"
+                        | "killbgscripts"
+                        | "load"
+                        | "load_ext"
+                        | "loadpy"
+                        | "logoff"
+                        | "logon"
+                        | "logstart"
+                        | "logstate"
+                        | "logstop"
+                        | "lsmagic"
+                        | "macro"
+                        | "magic"
+                        | "mamba"
+                        | "matplotlib"
+                        | "micromamba"
+                        | "notebook"
+                        | "page"
+                        | "pastebin"
+                        | "pdb"
+                        | "pdef"
+                        | "pdoc"
+                        | "pfile"
+                        | "pinfo"
+                        | "pinfo2"
+                        | "pip"
+                        | "popd"
+                        | "pprint"
+                        | "precision"
+                        | "prun"
+                        | "psearch"
+                        | "psource"
+                        | "pushd"
+                        | "pwd"
+                        | "pycat"
+                        | "pylab"
+                        | "quickref"
+                        | "recall"
+                        | "rehashx"
+                        | "reload_ext"
+                        | "rerun"
+                        | "reset"
+                        | "reset_selective"
+                        | "run"
+                        | "save"
+                        | "sc"
+                        | "set_env"
+                        | "sx"
+                        | "system"
+                        | "tb"
+                        | "time"
+                        | "timeit"
+                        | "unalias"
+                        | "unload_ext"
+                        | "who"
+                        | "who_ls"
+                        | "whos"
+                        | "xdel"
+                        | "xmode"
+                )
+            })
+        {
+            return true;
         }
+
+        // Detect cell magics (which operate on multiple lines).
+        lines.any(|line| line.trim_start().starts_with("%%"))
     }
 }
 
@@ -481,6 +593,10 @@ mod tests {
     #[test_case(Path::new("code_and_magic.json"), true; "code_and_magic")]
     #[test_case(Path::new("only_code.json"), true; "only_code")]
     #[test_case(Path::new("cell_magic.json"), false; "cell_magic")]
+    #[test_case(Path::new("automagic.json"), false; "automagic")]
+    #[test_case(Path::new("automagics.json"), false; "automagics")]
+    #[test_case(Path::new("automagic_before_code.json"), false; "automagic_before_code")]
+    #[test_case(Path::new("automagic_after_code.json"), true; "automagic_after_code")]
     fn test_is_valid_code_cell(path: &Path, expected: bool) -> Result<()> {
         /// Read a Jupyter cell from the `resources/test/fixtures/jupyter/cell` directory.
         fn read_jupyter_cell(path: impl AsRef<Path>) -> Result<Cell> {