diff --git a/.changeset/five-chefs-report.md b/.changeset/five-chefs-report.md
new file mode 100644
index 0000000000..2954415d26
--- /dev/null
+++ b/.changeset/five-chefs-report.md
@@ -0,0 +1,5 @@
+---
+"@pnpm/plugin-commands-patching": minor
+---
+
+`pnpm patch-remove` removes the directory containing the patch file if it is empty.
diff --git a/patching/plugin-commands-patching/src/patchRemove.ts b/patching/plugin-commands-patching/src/patchRemove.ts
index 3bdf0cc489..33dd8339d0 100644
--- a/patching/plugin-commands-patching/src/patchRemove.ts
+++ b/patching/plugin-commands-patching/src/patchRemove.ts
@@ -57,9 +57,11 @@ export async function handler (opts: PatchRemoveCommandOptions, params: string[]
     throw new PnpmError('NO_PATCHES_TO_REMOVE', 'There are no patches that need to be removed')
   }
 
+  const patchesDirs = new Set<string>()
   await Promise.all(patchesToRemove.map(async (patch) => {
     if (Object.prototype.hasOwnProperty.call(patchedDependencies, patch)) {
       const patchFile = path.join(lockfileDir, patchedDependencies[patch])
+      patchesDirs.add(path.dirname(patchFile))
       await fs.rm(patchFile, { force: true })
       delete rootProjectManifest.pnpm!.patchedDependencies![patch]
       if (!Object.keys(rootProjectManifest.pnpm!.patchedDependencies!).length) {
@@ -71,6 +73,15 @@ export async function handler (opts: PatchRemoveCommandOptions, params: string[]
     }
   }))
 
+  await Promise.all(Array.from(patchesDirs).map(async (dir) => {
+    try {
+      const files = await fs.readdir(dir)
+      if (!files.length) {
+        await fs.rmdir(dir)
+      }
+    } catch {}
+  }))
+
   await writeProjectManifest(rootProjectManifest)
 
   if (opts?.selectedProjectsGraph?.[lockfileDir]) {
diff --git a/patching/plugin-commands-patching/test/patch.test.ts b/patching/plugin-commands-patching/test/patch.test.ts
index 2393371873..225aee3f99 100644
--- a/patching/plugin-commands-patching/test/patch.test.ts
+++ b/patching/plugin-commands-patching/test/patch.test.ts
@@ -898,6 +898,7 @@ describe('patch-remove', () => {
     const { manifest: newManifest } = await readProjectManifest(process.cwd())
     expect(newManifest!.pnpm!).toBeUndefined()
     expect(fs.existsSync(path.join(process.cwd(), 'patches/is-positive@1.0.0.patch'))).toBe(false)
+    expect(fs.existsSync(path.join(process.cwd(), 'patches'))).toBe(false)
   })
 
   test('prompt to select patches that to be removed', async () => {