diff --git a/apps/web/src/components/BranchToolbar.logic.test.ts b/apps/web/src/components/BranchToolbar.logic.test.ts
index 143b0a59b7143..99ae0bda81bba 100644
--- a/apps/web/src/components/BranchToolbar.logic.test.ts
+++ b/apps/web/src/components/BranchToolbar.logic.test.ts
@@ -8,6 +8,7 @@ import {
   resolveDraftEnvModeAfterBranchChange,
   resolveEffectiveEnvMode,
   resolveBranchToolbarPrBranch,
+  resolveConfirmedSelectedRef,
   resolveDefaultWorktreeBaseBranch,
   resolveLocalCheckoutBranchMismatch,
   resolveLockedWorkspaceLabel,
@@ -406,3 +407,28 @@ describe("sanitizeNewRefName", () => {
     expect(sanitizeNewRefName("foo--bar")).toBe("foo--bar");
   });
 });
+
+describe("resolveConfirmedSelectedRef", () => {
+  const listed: VcsRef = {
+    name: "previous",
+    isRemote: false,
+    current: false,
+    isDefault: false,
+    worktreePath: "/worktree-b",
+  };
+
+  it.each([
+    [
+      "the claimed worktree still has it checked out",
+      [{ ...listed, current: true }],
+      "/worktree-b",
+    ],
+    ["the claimed worktree has moved to another branch", [], null],
+    ["the claimed worktree lists it but not as current", [listed], null],
+    ["the read failed", null, null],
+  ] as const)("%s", (_label, refs, expected) => {
+    expect(resolveConfirmedSelectedRef(listed, refs === null ? null : { refs }).worktreePath).toBe(
+      expected,
+    );
+  });
+});
diff --git a/apps/web/src/components/BranchToolbar.logic.ts b/apps/web/src/components/BranchToolbar.logic.ts
index 78b1bff4aff4d..f47ddd63348b2 100644
--- a/apps/web/src/components/BranchToolbar.logic.ts
+++ b/apps/web/src/components/BranchToolbar.logic.ts
@@ -288,6 +288,20 @@ export function resolveLocalCheckoutBranchMismatch(input: {
   return { threadBranch: activeThreadBranch, currentBranch: currentGitBranch };
 }
 
+/**
+ * Keeps a picked ref's worktree claim only when a read in that worktree finds it checked out.
+ * `freshRead` is `null` when the read failed.
+ */
+export function resolveConfirmedSelectedRef(
+  listedRef: VcsRef,
+  freshRead: { readonly refs: ReadonlyArray<VcsRef> } | null,
+): VcsRef {
+  const checkedOut =
+    freshRead?.refs.some((ref) => ref.name === listedRef.name && !ref.isRemote && ref.current) ??
+    false;
+  return checkedOut ? listedRef : { ...listedRef, worktreePath: null };
+}
+
 export function resolveBranchSelectionTarget(input: {
   activeProjectCwd: string;
   activeProjectCheckoutRoot?: string | undefined;
diff --git a/apps/web/src/components/BranchToolbarBranchSelector.tsx b/apps/web/src/components/BranchToolbarBranchSelector.tsx
index 02fa9de2e716c..535a075202019 100644
--- a/apps/web/src/components/BranchToolbarBranchSelector.tsx
+++ b/apps/web/src/components/BranchToolbarBranchSelector.tsx
@@ -20,6 +20,7 @@ import {
   useEffectEvent,
   useImperativeHandle,
   useOptimistic,
+  useRef,
   useState,
   useTransition,
   type MouseEvent as ReactMouseEvent,
@@ -53,6 +54,7 @@ import {
   resolveBranchToolbarPrBranch,
   resolveBranchSelectionTarget,
   resolveBranchToolbarValue,
+  resolveConfirmedSelectedRef,
   resolveDefaultWorktreeBaseBranch,
   resolveDraftEnvModeAfterBranchChange,
   resolveEffectiveEnvMode,
@@ -130,6 +132,9 @@ export function BranchToolbarBranchSelector({
   const switchRef = useAtomCommand(vcsEnvironment.switchRef, {
     reportFailure: false,
   });
+  const readRefs = useAtomCommand(vcsEnvironment.readRefs, {
+    reportFailure: false,
+  });
   const refreshLocalStatusForPicker = useAtomCommand(vcsEnvironment.refreshLocalStatusForPicker, {
     reportFailure: false,
   });
@@ -423,17 +428,40 @@ export function BranchToolbarBranchSelector({
     });
   };
 
-  const selectBranch = (refName: VcsRef) => {
+  // The picker's list, and the server's coalesced ref listing, can predate a checkout an agent
+  // ran itself. Only the claimed worktree's live HEAD confirms the claim; an unconfirmed one
+  // falls back to a real checkout, which Git refuses if the branch is checked out elsewhere.
+  const latestSelectionIdRef = useRef(0);
+  const readSelectedRef = async (worktreePath: string, listedRef: VcsRef): Promise<VcsRef> => {
+    const result = await readRefs({
+      environmentId,
+      input: { cwd: worktreePath, query: listedRef.name, refKind: "local", limit: 1 },
+    });
+    return resolveConfirmedSelectedRef(listedRef, result._tag === "Success" ? result.value : null);
+  };
+
+  const selectBranch = async (listedRef: VcsRef) => {
     if (!canUpdateThreadBranch || !branchCwd || !activeProjectCwd || isBranchActionPending) return;
+    const selectionId = ++latestSelectionIdRef.current;
 
-    const latest = readLatestThreadState();
+    let latest = readLatestThreadState();
     if (isSelectingWorktreeBase) {
       if (latest.worktreePath) return;
-      setThreadBranch(refName.name, null);
+      setThreadBranch(listedRef.name, null);
       setIsBranchMenuOpen(false);
       onComposerFocusRequest?.();
       return;
     }
+
+    setIsBranchMenuOpen(false);
+    onComposerFocusRequest?.();
+
+    const refName = listedRef.worktreePath
+      ? await readSelectedRef(listedRef.worktreePath, listedRef)
+      : listedRef;
+    // A later pick made while this one was confirming its worktree wins.
+    if (selectionId !== latestSelectionIdRef.current) return;
+    latest = readLatestThreadState();
     const selectionTarget = resolveBranchSelectionTarget({
       activeProjectCwd,
       activeProjectCheckoutRoot,
@@ -455,8 +483,6 @@ export function BranchToolbarBranchSelector({
       !(selectionTarget.staysInActiveCheckout && canWriteSourceControl)
     ) {
       setThreadBranch(refName.name, selectionTarget.nextWorktreePath);
-      setIsBranchMenuOpen(false);
-      onComposerFocusRequest?.();
       return;
     }
 
@@ -464,9 +490,6 @@ export function BranchToolbarBranchSelector({
       ? deriveLocalBranchNameFromRemoteRef(refName.name)
       : refName.name;
 
-    setIsBranchMenuOpen(false);
-    onComposerFocusRequest?.();
-
     runBranchAction(async () => {
       const previousBranch = resolvedActiveBranch;
       setOptimisticBranch(selectedBranchName);
@@ -531,6 +554,7 @@ export function BranchToolbarBranchSelector({
     if (!canChangeThreadBranch) return;
     const name = sanitizeNewRefName(rawName);
     if (!branchCwd || !name || isBranchActionPending) return;
+    latestSelectionIdRef.current++;
 
     setIsBranchMenuOpen(false);
     onComposerFocusRequest?.();
@@ -667,6 +691,7 @@ export function BranchToolbarBranchSelector({
 
   function selectPickerItem(itemValue: string) {
     if (itemValue === checkoutPullRequestItemValue && prReference && onCheckoutPullRequestRequest) {
+      latestSelectionIdRef.current++;
       handleOpenChange(false);
       onComposerFocusRequest?.();
       onCheckoutPullRequestRequest(prReference);
@@ -674,7 +699,7 @@ export function BranchToolbarBranchSelector({
       createRef(trimmedBranchQuery);
     } else {
       const refName = branchByName.get(itemValue);
-      if (refName) selectBranch(refName);
+      if (refName) void selectBranch(refName);
     }
   }