diff --git a/src/main/ipc/worktrees.test.ts b/src/main/ipc/worktrees.test.ts
index 6d098fb9079..44b8beaaba2 100644
--- a/src/main/ipc/worktrees.test.ts
+++ b/src/main/ipc/worktrees.test.ts
@@ -18,7 +18,8 @@ const {
   hasHooksFileMock,
   loadHooksMock,
   computeWorktreePathMock,
-  ensurePathWithinWorkspaceMock
+  ensurePathWithinWorkspaceMock,
+  gitExecFileAsyncMock
 } = vi.hoisted(() => ({
   handleMock: vi.fn(),
   removeHandlerMock: vi.fn(),
@@ -36,7 +37,8 @@ const {
   hasHooksFileMock: vi.fn(),
   loadHooksMock: vi.fn(),
   computeWorktreePathMock: vi.fn(),
-  ensurePathWithinWorkspaceMock: vi.fn()
+  ensurePathWithinWorkspaceMock: vi.fn(),
+  gitExecFileAsyncMock: vi.fn()
 }))
 
 vi.mock('electron', () => ({
@@ -52,6 +54,11 @@ vi.mock('../git/worktree', () => ({
   removeWorktree: removeWorktreeMock
 }))
 
+vi.mock('../git/runner', () => ({
+  gitExecFileAsync: gitExecFileAsyncMock,
+  gitExecFileSync: vi.fn()
+}))
+
 vi.mock('../git/repo', () => ({
   getGitUsername: getGitUsernameMock,
   getDefaultBaseRef: getDefaultBaseRefMock,
@@ -120,6 +127,7 @@ describe('registerWorktreeHandlers', () => {
       loadHooksMock,
       computeWorktreePathMock,
       ensurePathWithinWorkspaceMock,
+      gitExecFileAsyncMock,
       mainWindow.webContents.send,
       store.getRepos,
       store.getRepo,
@@ -350,6 +358,28 @@ describe('registerWorktreeHandlers', () => {
     })
   })
 
+  it('prunes git worktree tracking when removing an orphaned worktree', async () => {
+    const orphanError = Object.assign(new Error('git worktree remove failed'), {
+      stderr: "fatal: '/workspace/feature-wt' is not a working tree"
+    })
+    removeWorktreeMock.mockRejectedValue(orphanError)
+    getEffectiveHooksMock.mockReturnValue(null)
+    gitExecFileAsyncMock.mockResolvedValue({ stdout: '', stderr: '' })
+
+    await handlers['worktrees:remove'](null, {
+      worktreeId: 'repo-1::/workspace/feature-wt'
+    })
+
+    // Should have called git worktree prune to clean up stale tracking
+    expect(gitExecFileAsyncMock).toHaveBeenCalledWith(['worktree', 'prune'], {
+      cwd: '/workspace/repo'
+    })
+    expect(store.removeWorktreeMeta).toHaveBeenCalledWith('repo-1::/workspace/feature-wt')
+    expect(mainWindow.webContents.send).toHaveBeenCalledWith('worktrees:changed', {
+      repoId: 'repo-1'
+    })
+  })
+
   it('rejects ask-policy creates before mutating git state when setup decision is missing', async () => {
     getEffectiveHooksMock.mockReturnValue({
       scripts: {
diff --git a/src/main/ipc/worktrees.ts b/src/main/ipc/worktrees.ts
index 91235b3cd4c..6fe616aa626 100644
--- a/src/main/ipc/worktrees.ts
+++ b/src/main/ipc/worktrees.ts
@@ -12,7 +12,7 @@ import type {
 import { getPRForBranch } from '../github/client'
 import { listWorktrees, addWorktree, removeWorktree } from '../git/worktree'
 import { getGitUsername, getDefaultBaseRef, getBranchConflictKind } from '../git/repo'
-import { gitExecFileSync } from '../git/runner'
+import { gitExecFileAsync, gitExecFileSync } from '../git/runner'
 import { isWslPath, parseWslPath, getWslHome } from '../wsl'
 import { join } from 'path'
 import { listRepoWorktrees } from '../repo-worktrees'
@@ -242,6 +242,11 @@ export function registerWorktreeHandlers(mainWindow: BrowserWindow, store: Store
         if (isOrphanedWorktreeError(error)) {
           console.warn(`[worktrees] Orphaned worktree detected at ${worktreePath}, cleaning up`)
           await rm(worktreePath, { recursive: true, force: true }).catch(() => {})
+          // Why: `git worktree remove` failed, so git's internal worktree tracking
+          // (`.git/worktrees/<name>`) is still intact. Without pruning, `git worktree
+          // list` continues to show the stale entry and the branch it had checked out
+          // remains locked — other worktrees cannot check it out.
+          await gitExecFileAsync(['worktree', 'prune'], { cwd: repo.path }).catch(() => {})
           store.removeWorktreeMeta(args.worktreeId)
           await rebuildAuthorizedRootsCache(store)
           notifyWorktreesChanged(mainWindow, repoId)
diff --git a/src/main/runtime/orca-runtime.ts b/src/main/runtime/orca-runtime.ts
index ee93c565d56..7dfba77252e 100644
--- a/src/main/runtime/orca-runtime.ts
+++ b/src/main/runtime/orca-runtime.ts
@@ -1,7 +1,7 @@
 /* eslint-disable max-lines -- Why: the Orca runtime is the authoritative live control plane for the CLI, so handle validation, selector resolution, wait state, and summaries are kept together to avoid split-brain behavior. */
 /* eslint-disable unicorn/no-useless-spread -- Why: waiter sets and handle keys are cloned intentionally before mutation so resolution and rejection can safely remove entries while iterating. */
 /* eslint-disable no-control-regex -- Why: terminal normalization must strip ANSI and OSC control sequences from PTY output before returning bounded text to agents. */
-import { gitExecFileSync } from '../git/runner'
+import { gitExecFileAsync, gitExecFileSync } from '../git/runner'
 import { isWslPath, parseWslPath, getWslHome } from '../wsl'
 import { randomUUID } from 'crypto'
 import { join } from 'path'
@@ -738,6 +738,11 @@ export class OrcaRuntimeService {
     } catch (error) {
       if (isOrphanedWorktreeError(error)) {
         await rm(worktree.path, { recursive: true, force: true }).catch(() => {})
+        // Why: `git worktree remove` failed, so git's internal worktree tracking
+        // (`.git/worktrees/<name>`) is still intact. Without pruning, `git worktree
+        // list` continues to show the stale entry and the branch it had checked out
+        // remains locked — other worktrees cannot check it out.
+        await gitExecFileAsync(['worktree', 'prune'], { cwd: repo.path }).catch(() => {})
         this.store.removeWorktreeMeta(worktree.id)
         this.invalidateResolvedWorktreeCache()
         this.notifier?.worktreesChanged(repo.id)