diff --git a/.changeset/shy-weeks-raise.md b/.changeset/shy-weeks-raise.md
new file mode 100644
index 0000000000..7fe0bc68d7
--- /dev/null
+++ b/.changeset/shy-weeks-raise.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/plugin-commands-store": patch
+"pnpm": patch
+---
+
+`pnpm store prune` should not fail if the dlx cache directory has files, not only directories [#10384](https://github.com/pnpm/pnpm/pull/10384)
diff --git a/store/plugin-commands-store/src/cleanExpiredDlxCache.test.ts b/store/plugin-commands-store/src/cleanExpiredDlxCache.test.ts
index 221f28d5b8..f1b448c4d7 100644
--- a/store/plugin-commands-store/src/cleanExpiredDlxCache.test.ts
+++ b/store/plugin-commands-store/src/cleanExpiredDlxCache.test.ts
@@ -192,3 +192,31 @@ test("cleanOrphans deletes dirs that don't contain `link` and subdirs that aren'
   // expecting directory that doesn't contain `link` to be deleted.
   expect(fs.existsSync(path.join(cacheDir, 'dlx', createCacheKey('bar')))).toBe(false)
 })
+
+test('cleanExpiredDlxCache ignores files in the dlx cache directory', async () => {
+  prepareEmpty()
+
+  const cacheDir = path.resolve('cache')
+  const dlxCacheMaxAge = 0
+  const now = new Date()
+
+  // Create a directory that should be cleaned
+  createSampleDlxCacheItem(cacheDir, 'foo', now, 1)
+
+  // Create a file in the dlx directory (simulating the bug/noise)
+  const dlxDir = path.join(cacheDir, 'dlx')
+  fsOriginal.mkdirSync(dlxDir, { recursive: true })
+  fsOriginal.writeFileSync(path.join(dlxDir, 'some-random-file'), 'hello')
+
+  await cleanExpiredDlxCache({
+    cacheDir,
+    dlxCacheMaxAge,
+    now,
+  })
+
+  // The directory should be gone (cleaned)
+  expect(fsOriginal.existsSync(path.join(dlxDir, createCacheKey('foo')))).toBeFalsy()
+
+  // The file should still be there (ignored)
+  expect(fsOriginal.existsSync(path.join(dlxDir, 'some-random-file'))).toBeTruthy()
+})
diff --git a/store/plugin-commands-store/src/cleanExpiredDlxCache.ts b/store/plugin-commands-store/src/cleanExpiredDlxCache.ts
index 11cf0270df..c7af911f27 100644
--- a/store/plugin-commands-store/src/cleanExpiredDlxCache.ts
+++ b/store/plugin-commands-store/src/cleanExpiredDlxCache.ts
@@ -74,7 +74,16 @@ async function getStats (path: string): Promise<Stats | 'ENOENT'> {
 
 function readOptDir (dirPath: string): string[] | null {
   try {
-    return readdirSync(dirPath, 'utf-8')
+    const dirEntries: string[] = []
+    for (const entry of readdirSync(dirPath, {
+      encoding: 'utf-8',
+      withFileTypes: true,
+    })) {
+      if (entry.isDirectory()) {
+        dirEntries.push(entry.name)
+      }
+    }
+    return dirEntries
   } catch (err) {
     if (util.types.isNativeError(err) && 'code' in err && err.code === 'ENOENT') {
       return null