diff --git a/cmd/sync.go b/cmd/sync.go
index 3ac1e81..adc15d4 100644
--- a/cmd/sync.go
+++ b/cmd/sync.go
@@ -511,7 +511,14 @@ func runSync(gitClient git.GitClient, githubClient github.GitHubClient, syncRemo
 		} else if _, exists := prCache[branch.Name]; !exists {
 			// No PR found - check if branch was merged via git history
 			remoteBase := syncRemote + "/" + baseBranch
-			if merged, err := gitClient.IsAncestor(branch.Name, remoteBase); err == nil && merged {
+			merged, err := gitClient.IsAncestor(branch.Name, remoteBase)
+			// If branch is ancestor of remote base, also check reverse: if both are ancestors
+			// of each other, they point to the same commit — a new branch with no commits, not merged
+			sameCommit := false
+			if err == nil && merged {
+				sameCommit, _ = gitClient.IsAncestor(remoteBase, branch.Name)
+			}
+			if err == nil && merged && !sameCommit {
 				fmt.Printf("%s Skipping %s (merged into %s, detected via git history)...\n", progress, ui.Branch(branch.Name), ui.Branch(baseBranch))
 				fmt.Printf("  Removing from stack tracking...\n")
 				configKey := fmt.Sprintf("branch.%s.stackparent", branch.Name)
@@ -540,7 +547,12 @@ func runSync(gitClient git.GitClient, githubClient github.GitHubClient, syncRemo
 		} else if parentPR == nil && branch.Parent != baseBranch {
 			// No PR found for parent - check if parent was merged via git history
 			remoteBase := syncRemote + "/" + baseBranch
-			if merged, err := gitClient.IsAncestor(branch.Parent, remoteBase); err == nil && merged {
+			merged, err := gitClient.IsAncestor(branch.Parent, remoteBase)
+			sameCommit := false
+			if err == nil && merged {
+				sameCommit, _ = gitClient.IsAncestor(remoteBase, branch.Parent)
+			}
+			if err == nil && merged && !sameCommit {
 				fmt.Printf("  Parent %s appears merged into %s (detected via git history)\n", ui.Branch(branch.Parent), ui.Branch(baseBranch))
 				oldParent = branch.Parent
 				parentMergedViaGit = true
diff --git a/cmd/sync_test.go b/cmd/sync_test.go
index 17bafee..081d2d1 100644
--- a/cmd/sync_test.go
+++ b/cmd/sync_test.go
@@ -1236,6 +1236,8 @@ func TestRunSyncGitBasedMergeDetection(t *testing.T) {
 
 		// feature-a: no PR, but IsAncestor returns true → merged via git history
 		mockGit.On("IsAncestor", "feature-a", "origin/main").Return(true, nil)
+		// Reverse check: origin/main is NOT ancestor of feature-a (branch has diverged, truly merged)
+		mockGit.On("IsAncestor", "origin/main", "feature-a").Return(false, nil)
 		// Remove feature-a from stack
 		mockGit.On("UnsetConfig", "branch.feature-a.stackparent").Return(nil)
 
@@ -1244,6 +1246,7 @@ func TestRunSyncGitBasedMergeDetection(t *testing.T) {
 
 		// feature-b's parent (feature-a) has no PR, parent merged via git
 		// IsAncestor("feature-a", "origin/main") already mocked above → true
+		// IsAncestor("origin/main", "feature-a") already mocked above → false (truly merged)
 
 		// Reparent feature-b from feature-a to main
 		mockGit.On("GetConfig", "branch.feature-a.stackparent").Return("main")
@@ -1275,6 +1278,66 @@ func TestRunSyncGitBasedMergeDetection(t *testing.T) {
 		mockGH.AssertExpectations(t)
 	})
 
+	t.Run("branch with no commits is not treated as merged", func(t *testing.T) {
+		mockGit := new(testutil.MockGitClient)
+		mockGH := new(testutil.MockGitHubClient)
+
+		// Setup: no existing sync state
+		mockGit.On("GetConfig", "stack.sync.stashed").Return("")
+		mockGit.On("GetConfig", "stack.sync.originalBranch").Return("")
+		mockGit.On("GetCurrentBranch").Return("feature-a", nil)
+		mockGit.On("SetConfig", "stack.sync.originalBranch", "feature-a").Return(nil)
+		mockGit.On("IsWorkingTreeClean").Return(true, nil)
+		mockGit.On("GetConfig", "branch.feature-a.stackparent").Return("main")
+		mockGit.On("GetConfig", "stack.baseBranch").Return("").Maybe()
+		mockGit.On("GetDefaultBranch").Return("main").Maybe()
+
+		stackParents := map[string]string{
+			"feature-a": "main",
+		}
+		mockGit.On("GetAllStackParents").Return(stackParents, nil).Maybe()
+
+		// No PRs found
+		mockGit.On("FetchRemote", "origin").Return(nil)
+		mockGH.On("GetPRsForBranches", mock.Anything).Return(make(map[string]*github.PRInfo))
+
+		mockGit.On("GetWorktreeBranches").Return(make(map[string]string), nil)
+		mockGit.On("GetCurrentWorktreePath").Return("/Users/test/repo", nil)
+		mockGit.On("GetRemoteBranchesSet").Return(map[string]bool{
+			"main":      true,
+			"feature-a": true,
+		})
+
+		// feature-a has no commits: both IsAncestor directions return true (same commit)
+		mockGit.On("IsAncestor", "feature-a", "origin/main").Return(true, nil)
+		mockGit.On("IsAncestor", "origin/main", "feature-a").Return(true, nil)
+
+		// Branch should NOT be removed — should proceed to normal processing
+		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
+		mockGit.On("GetCommitHash", "feature-a").Return("main123", nil)
+		mockGit.On("GetCommitHash", "origin/feature-a").Return("main123", nil)
+		mockGit.On("FetchBranchFromRemote", "origin", "main").Return(nil)
+		mockGit.On("GetUniqueCommitsByPatch", "origin/main", "feature-a").Return([]string{}, nil)
+		mockGit.On("Rebase", "origin/main").Return(nil)
+		mockGit.On("FetchBranch", "feature-a").Return(nil)
+		mockGit.On("PushWithExpectedRemote", "feature-a", "main123").Return(nil)
+
+		// Return to original branch
+		mockGit.On("CheckoutBranch", "feature-a").Return(nil)
+		// Clean up sync state
+		mockGit.On("UnsetConfig", "stack.sync.stashed").Return(nil)
+		mockGit.On("UnsetConfig", "stack.sync.originalBranch").Return(nil)
+		mockGit.On("GetConfig", "stack.postSyncInstall").Return("false").Maybe()
+
+		err := runSync(mockGit, mockGH, "origin")
+
+		assert.NoError(t, err)
+		// Verify branch was NOT removed from stack tracking
+		mockGit.AssertNotCalled(t, "UnsetConfig", "branch.feature-a.stackparent")
+		mockGit.AssertExpectations(t)
+		mockGH.AssertExpectations(t)
+	})
+
 	t.Run("branch not merged via git is processed normally", func(t *testing.T) {
 		mockGit := new(testutil.MockGitClient)
 		mockGH := new(testutil.MockGitHubClient)