diff --git a/apps/web/src/components/BranchToolbar.logic.test.ts b/apps/web/src/components/BranchToolbar.logic.test.ts
index d1ca6d01e4c34..7e7e225e67c7f 100644
--- a/apps/web/src/components/BranchToolbar.logic.test.ts
+++ b/apps/web/src/components/BranchToolbar.logic.test.ts
@@ -8,6 +8,7 @@ import {
   resolveEffectiveEnvMode,
   resolveBranchToolbarPrBranch,
   resolveLocalCheckoutBranchMismatch,
+  resolveWorktreeBaseBranchCandidate,
   sanitizeNewRefName,
   shouldIncludeBranchPickerItem,
 } from "./BranchToolbar.logic";
@@ -254,3 +255,53 @@ describe("sanitizeNewRefName", () => {
     expect(sanitizeNewRefName("foo--bar")).toBe("foo--bar");
   });
 });
+
+describe("resolveWorktreeBaseBranchCandidate", () => {
+  const ref = (name: string, overrides: Partial<VcsRef> = {}): VcsRef => ({
+    name,
+    current: false,
+    isDefault: false,
+    worktreePath: null,
+    ...overrides,
+  });
+
+  it("waits for the initial ref list", () => {
+    expect(
+      resolveWorktreeBaseBranchCandidate({
+        isInitialBranchesLoadPending: true,
+        refs: [],
+        currentGitBranch: "staging",
+      }),
+    ).toBeNull();
+  });
+
+  it("prefers the default branch", () => {
+    expect(
+      resolveWorktreeBaseBranchCandidate({
+        isInitialBranchesLoadPending: false,
+        refs: [ref("feature", { current: true }), ref("staging", { isDefault: true })],
+        currentGitBranch: "feature",
+      }),
+    ).toBe("staging");
+  });
+
+  it("falls back to the current branch when it is a listed ref", () => {
+    expect(
+      resolveWorktreeBaseBranchCandidate({
+        isInitialBranchesLoadPending: false,
+        refs: [ref("develop", { current: true })],
+        currentGitBranch: "develop",
+      }),
+    ).toBe("develop");
+  });
+
+  it("ignores an unborn HEAD while a clone is still running", () => {
+    expect(
+      resolveWorktreeBaseBranchCandidate({
+        isInitialBranchesLoadPending: false,
+        refs: [],
+        currentGitBranch: "main",
+      }),
+    ).toBeNull();
+  });
+});
diff --git a/apps/web/src/components/BranchToolbar.logic.ts b/apps/web/src/components/BranchToolbar.logic.ts
index 01b9155617a44..560be9fe4b9ed 100644
--- a/apps/web/src/components/BranchToolbar.logic.ts
+++ b/apps/web/src/components/BranchToolbar.logic.ts
@@ -200,6 +200,23 @@ export function resolveBranchToolbarValue(input: {
   return currentGitBranch ?? activeThreadBranch;
 }
 
+// A repository whose HEAD is unborn (e.g. while a clone is still running) reports its
+// init.defaultBranch as the current branch even though no such ref exists yet.
+export function resolveWorktreeBaseBranchCandidate(input: {
+  isInitialBranchesLoadPending: boolean;
+  refs: ReadonlyArray<VcsRef>;
+  currentGitBranch: string | null;
+}): string | null {
+  const { isInitialBranchesLoadPending, refs, currentGitBranch } = input;
+  if (isInitialBranchesLoadPending) return null;
+  const defaultBranchName = refs.find((refName) => refName.isDefault)?.name ?? null;
+  if (defaultBranchName) return defaultBranchName;
+  if (currentGitBranch && refs.some((refName) => refName.name === currentGitBranch)) {
+    return currentGitBranch;
+  }
+  return null;
+}
+
 export function resolveBranchTriggerLabel(input: {
   activeWorktreePath: string | null;
   effectiveEnvMode: EnvMode;
diff --git a/apps/web/src/components/BranchToolbarBranchSelector.tsx b/apps/web/src/components/BranchToolbarBranchSelector.tsx
index 60eef31b1b63d..19328d3967fd6 100644
--- a/apps/web/src/components/BranchToolbarBranchSelector.tsx
+++ b/apps/web/src/components/BranchToolbarBranchSelector.tsx
@@ -53,6 +53,7 @@ import {
   resolveBranchToolbarValue,
   resolveDraftEnvModeAfterBranchChange,
   resolveEffectiveEnvMode,
+  resolveWorktreeBaseBranchCandidate,
   sanitizeNewRefName,
   shouldIncludeBranchPickerItem,
 } from "./BranchToolbar.logic";
@@ -252,7 +253,6 @@ export function BranchToolbarBranchSelector({
   const createBranchItemValue = canCreateBranch
     ? `__create_new_branch__:${trimmedBranchQuery}`
     : null;
-  const defaultBranchName = refs.find((refName) => refName.isDefault)?.name ?? null;
   const pickerCreateBranchItemValue = hasExactBranchMatch ? null : createBranchItemValue;
   const branchPickerItems = [
     ...(checkoutPullRequestItemValue ? [checkoutPullRequestItemValue] : []),
@@ -478,9 +478,11 @@ export function BranchToolbarBranchSelector({
     });
   };
 
-  const worktreeBaseBranchCandidate = isInitialBranchesLoadPending
-    ? null
-    : (defaultBranchName ?? currentGitBranch);
+  const worktreeBaseBranchCandidate = resolveWorktreeBaseBranchCandidate({
+    isInitialBranchesLoadPending,
+    refs,
+    currentGitBranch,
+  });
 
   // The server sets started threads' branches; defaulting here would detach the agent from its worktree.
   const threadStarted = serverSession !== null;