diff --git a/e2e_tests/sync_all_deleted_branch_test.go b/e2e_tests/sync_all_deleted_branch_test.go
new file mode 100644
index 00000000..e7813a72
--- /dev/null
+++ b/e2e_tests/sync_all_deleted_branch_test.go
@@ -0,0 +1,42 @@
+package e2e_tests
+
+import (
+	"testing"
+
+	"github.com/aviator-co/av/internal/git/gittest"
+)
+
+func TestSyncAllWithDeletedBranch(t *testing.T) {
+	server := RunMockGitHubServer(t)
+	defer server.Close()
+	repo := gittest.NewTempRepoWithGitHubServer(t, server.URL)
+	Chdir(t, repo.RepoDir)
+
+	// Create two independent stacks off main.
+	repo.Git(t, "switch", "main")
+	RequireAv(t, "branch", "stack-1")
+	repo.CommitFile(t, "my-file", "1a\n", gittest.WithMessage("Commit 1a"))
+
+	repo.Git(t, "switch", "main")
+	RequireAv(t, "branch", "stack-2")
+	repo.CommitFile(t, "my-file-2", "2a\n", gittest.WithMessage("Commit 2a"))
+
+	// Delete stack-1's git ref without tidying av metadata.
+	// This simulates a branch deleted externally (e.g., on GitHub) but not yet
+	// cleaned up in av's internal database.
+	repo.Git(t, "switch", "stack-2")
+	repo.Git(t, "branch", "-D", "stack-1")
+
+	// Push a new commit to main so there's something to sync.
+	repo.WithCheckoutBranch(t, "refs/heads/main", func() {
+		repo.CommitFile(t, "other-file", "X2\n", gittest.WithMessage("Commit X2"))
+		repo.Git(t, "push", "origin", "main")
+	})
+
+	// This should succeed, skipping the deleted branch rather than failing
+	// with "error: git merge-base: exit status 128".
+	RequireAv(t, "sync", "--all", "--rebase-to-trunk")
+
+	// stack-2 should have been synced onto the latest main.
+	repo.Git(t, "merge-base", "--is-ancestor", "main", "stack-2")
+}
diff --git a/internal/sequencer/planner/targets.go b/internal/sequencer/planner/targets.go
index 029a27a6..dd3ae89b 100644
--- a/internal/sequencer/planner/targets.go
+++ b/internal/sequencer/planner/targets.go
@@ -43,11 +43,17 @@ func GetTargetBranches(
 				continue
 			}
 			if includeStackRoots {
-				ret = append(ret, plumbing.NewBranchReferenceName(br.Name))
+				ref := plumbing.NewBranchReferenceName(br.Name)
+				if exists, _ := repo.DoesRefExist(ctx, ref.String()); exists {
+					ret = append(ret, ref)
+				}
 			}
 			// Use filtered traversal to skip excluded branches and their descendants
 			for _, n := range meta.SubsequentBranchesFiltered(tx, br.Name, true) {
-				ret = append(ret, plumbing.NewBranchReferenceName(n))
+				ref := plumbing.NewBranchReferenceName(n)
+				if exists, _ := repo.DoesRefExist(ctx, ref.String()); exists {
+					ret = append(ret, ref)
+				}
 			}
 		}
 		return ret, nil