diff --git a/common/changes/@rushstack/eslint-patch/eslint-bulk-issues_2024-03-28-17-06.json b/common/changes/@rushstack/eslint-patch/eslint-bulk-issues_2024-03-28-17-06.json
new file mode 100644
index 00000000000..c3286b8f661
--- /dev/null
+++ b/common/changes/@rushstack/eslint-patch/eslint-bulk-issues_2024-03-28-17-06.json
@@ -0,0 +1,10 @@
+{
+  "changes": [
+    {
+      "packageName": "@rushstack/eslint-patch",
+      "comment": "Fix an issue with running `eslint-bulk prune` in a project with suppressions that refer to deleted files.",
+      "type": "patch"
+    }
+  ],
+  "packageName": "@rushstack/eslint-patch"
+}
\ No newline at end of file
diff --git a/eslint/eslint-patch/src/eslint-bulk-suppressions/cli/prune.ts b/eslint/eslint-patch/src/eslint-bulk-suppressions/cli/prune.ts
index 288cd1c36dd..9a3b727091a 100755
--- a/eslint/eslint-patch/src/eslint-bulk-suppressions/cli/prune.ts
+++ b/eslint/eslint-patch/src/eslint-bulk-suppressions/cli/prune.ts
@@ -1,6 +1,8 @@
 // Copyright (c) Microsoft Corporation. All rights reserved. Licensed under the MIT license.
 // See LICENSE in the project root for license information.
 
+import fs from 'fs';
+
 import { printPruneHelp } from './utils/print-help';
 import { runEslintAsync } from './runEslint';
 import { ESLINT_BULK_PRUNE_ENV_VAR_NAME } from '../constants';
@@ -20,13 +22,11 @@ export async function pruneAsync(): Promise<void> {
 
   process.env[ESLINT_BULK_PRUNE_ENV_VAR_NAME] = '1';
 
-  const allFiles: string[] = getAllFilesWithExistingSuppressionsForCwd();
-  console.log(`Pruning suppressions for ${allFiles.length} files...`);
-
+  const allFiles: string[] = await getAllFilesWithExistingSuppressionsForCwdAsync();
   await runEslintAsync(allFiles, 'prune');
 }
 
-function getAllFilesWithExistingSuppressionsForCwd(): string[] {
+async function getAllFilesWithExistingSuppressionsForCwdAsync(): Promise<string[]> {
   const { jsonObject: bulkSuppressionsConfigJson } = getSuppressionsConfigForEslintrcFolderPath(
     process.cwd().replace(/\\/g, '/')
   );
@@ -35,5 +35,28 @@ function getAllFilesWithExistingSuppressionsForCwd(): string[] {
     allFiles.add(filePath);
   }
 
-  return Array.from(allFiles);
+  const allFilesArray: string[] = Array.from(allFiles);
+
+  const allExistingFiles: string[] = [];
+  // TODO: limit parallelism here with something similar to `Async.forEachAsync` from `node-core-library`.
+  await Promise.all(
+    allFilesArray.map(async (filePath: string) => {
+      try {
+        await fs.promises.access(filePath, fs.constants.F_OK);
+        allExistingFiles.push(filePath);
+      } catch {
+        // Doesn't exist - ignore
+      }
+    })
+  );
+
+  console.log(`Found ${allExistingFiles.length} files with existing suppressions.`);
+  const deletedCount: number = allFilesArray.length - allExistingFiles.length;
+  if (deletedCount > 0) {
+    console.log(`${deletedCount} files with suppressions were deleted.`);
+  }
+
+  console.log(`Pruning suppressions for ${allExistingFiles.length} files...`);
+
+  return allExistingFiles;
 }