diff --git a/.changeset/gold-colts-brush.md b/.changeset/gold-colts-brush.md
new file mode 100644
index 0000000000..089a4545ce
--- /dev/null
+++ b/.changeset/gold-colts-brush.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/link-bins": patch
+"pnpm": patch
+---
+
+Fixed EISDIR error when bin field points to a directory [#9441](https://github.com/pnpm/pnpm/issues/9441).
diff --git a/cspell.json b/cspell.json
index 6e9cee2729..4d37bfb416 100644
--- a/cspell.json
+++ b/cspell.json
@@ -57,6 +57,7 @@
     "ebusy",
     "ehrkoext",
     "eintegrity",
+    "eisdir",
     "elifecycle",
     "elit",
     "emfile",
diff --git a/pkg-manager/link-bins/src/index.ts b/pkg-manager/link-bins/src/index.ts
index e4da2e902b..36114f5e86 100644
--- a/pkg-manager/link-bins/src/index.ts
+++ b/pkg-manager/link-bins/src/index.ts
@@ -284,7 +284,7 @@ async function linkBin (cmd: CommandInfo, binsDir: string, opts?: LinkBinOptions
       await symlinkDir(cmd.path, externalBinPath)
       await fixBin(cmd.path, 0o755)
     } catch (err: any) { // eslint-disable-line
-      if (err.code !== 'ENOENT') {
+      if (err.code !== 'ENOENT' && err.code !== 'EISDIR') {
         throw err
       }
       globalWarn(`Failed to create bin at ${externalBinPath}. ${err.message as string}`)
@@ -308,7 +308,7 @@ async function linkBin (cmd: CommandInfo, binsDir: string, opts?: LinkBinOptions
       nodeExecPath: cmd.nodeExecPath,
     })
   } catch (err: any) { // eslint-disable-line
-    if (err.code !== 'ENOENT') {
+    if (err.code !== 'ENOENT' && err.code !== 'EISDIR') {
       throw err
     }
     globalWarn(`Failed to create bin at ${externalBinPath}. ${err.message as string}`)
diff --git a/pkg-manager/link-bins/test/fixtures/bin-is-directory/.gitignore b/pkg-manager/link-bins/test/fixtures/bin-is-directory/.gitignore
new file mode 100644
index 0000000000..5867a0493e
--- /dev/null
+++ b/pkg-manager/link-bins/test/fixtures/bin-is-directory/.gitignore
@@ -0,0 +1,2 @@
+!**/node_modules/**/*
+!/node_modules/
diff --git a/pkg-manager/link-bins/test/fixtures/bin-is-directory/node_modules/invalid-bin/dist/readme.txt b/pkg-manager/link-bins/test/fixtures/bin-is-directory/node_modules/invalid-bin/dist/readme.txt
new file mode 100644
index 0000000000..d2de8bf8d9
--- /dev/null
+++ b/pkg-manager/link-bins/test/fixtures/bin-is-directory/node_modules/invalid-bin/dist/readme.txt
@@ -0,0 +1 @@
+This is a directory, not a file.
diff --git a/pkg-manager/link-bins/test/fixtures/bin-is-directory/node_modules/invalid-bin/package.json b/pkg-manager/link-bins/test/fixtures/bin-is-directory/node_modules/invalid-bin/package.json
new file mode 100644
index 0000000000..174040dbfa
--- /dev/null
+++ b/pkg-manager/link-bins/test/fixtures/bin-is-directory/node_modules/invalid-bin/package.json
@@ -0,0 +1,5 @@
+{
+  "name": "invalid-bin",
+  "version": "1.0.0",
+  "bin": "./dist"
+}
diff --git a/pkg-manager/link-bins/test/index.ts b/pkg-manager/link-bins/test/index.ts
index 9192808ee9..0449f3de99 100644
--- a/pkg-manager/link-bins/test/index.ts
+++ b/pkg-manager/link-bins/test/index.ts
@@ -32,6 +32,7 @@ const f = fixtures(__dirname)
 
 beforeEach(() => {
   jest.mocked(binsConflictLogger.debug).mockClear()
+  jest.mocked(globalWarn).mockClear()
 })
 
 const POWER_SHELL_IS_SUPPORTED = isWindows()
@@ -535,6 +536,17 @@ testOnWindows('linkBins() should remove an existing .exe file from the target di
   expect(fs.readdirSync(binTarget)).toEqual(getExpectedBins(['simple']))
 })
 
+test('linkBins() should handle bin field pointing to a directory gracefully', async () => {
+  const binTarget = tempy.directory()
+  const binIsDirFixture = f.prepare('bin-is-directory')
+  const warn = jest.fn()
+
+  await linkBins(path.join(binIsDirFixture, 'node_modules'), binTarget, { warn })
+
+  expect(fs.readdirSync(binTarget)).toEqual([])
+  expect(globalWarn).toHaveBeenCalled()
+})
+
 describe('enable prefer-symlinked-executables', () => {
   test('linkBins()', async () => {
     const binTarget = tempy.directory()