diff --git a/src/stack_pr/cli.py b/src/stack_pr/cli.py
index d068998..32afe35 100755
--- a/src/stack_pr/cli.py
+++ b/src/stack_pr/cli.py
@@ -69,6 +69,7 @@
     get_current_branch_name,
     get_gh_username,
     get_uncommitted_changes,
+    is_rebase_in_progress,
 )
 from stack_pr.shell_commands import (
     get_command_output,
@@ -170,6 +171,10 @@
 
 Please commit or stash them before working with stacks.
 """
+ERROR_REBASE_IN_PROGRESS = """Cannot submit while in the middle of a rebase.
+
+Please complete or abort the current rebase first.
+"""
 UPDATE_STACK_TIP = """
 If you'd like to push your local changes first, you can use the following command to update the stack:
   $ stack-pr export -B {top_commit}~{stack_size} -H {top_commit}"""
@@ -933,6 +938,11 @@ def command_submit(
             a draft.
     """
     log(h("SUBMIT"), level=1)
+
+    if is_rebase_in_progress():
+        error(ERROR_REBASE_IN_PROGRESS)
+        sys.exit(1)
+
     current_branch = get_current_branch_name()
 
     if should_update_local_base(
diff --git a/src/stack_pr/git.py b/src/stack_pr/git.py
index 3cb6ce3..cd4714a 100644
--- a/src/stack_pr/git.py
+++ b/src/stack_pr/git.py
@@ -213,3 +213,16 @@ def get_changed_dirs(
         files changed.
     """
     return {Path(file.parts[0]) for file in get_changed_files(base, repo_dir)}
+
+
+def is_rebase_in_progress(repo_dir: Path | None = None) -> bool:
+    """Check if a rebase operation is currently in progress.
+
+    Args:
+        repo_dir: path to the repo. Defaults to the current working directory.
+
+    Returns:
+        True if a rebase is in progress, False otherwise.
+    """
+    git_dir = Path(".git") if repo_dir is None else repo_dir / ".git"
+    return (git_dir / "rebase-merge").exists() or (git_dir / "rebase-apply").exists()
diff --git a/tests/test_misc.py b/tests/test_misc.py
index 93d8ee9..5517c10 100644
--- a/tests/test_misc.py
+++ b/tests/test_misc.py
@@ -1,4 +1,5 @@
 import sys
+import tempfile
 from pathlib import Path
 
 sys.path.append(str(Path(__file__).parent.parent / "src"))
@@ -12,7 +13,7 @@
     get_gh_username,
     get_taken_branch_ids,
 )
-from stack_pr.git import git_config
+from stack_pr.git import git_config, is_rebase_in_progress
 
 
 @pytest.fixture(scope="module")
@@ -90,3 +91,35 @@ def test_generate_available_branch_name() -> None:
         "refs/remotes/origin/TestBot-stack-134",
     ]
     assert generate_available_branch_name(refs, template) == "TestBot-stack-135"
+
+
+def test_is_rebase_in_progress() -> None:
+    """Test the is_rebase_in_progress function with different git states."""
+    with tempfile.TemporaryDirectory() as temp_dir:
+        repo_dir = Path(temp_dir)
+        git_dir = repo_dir / ".git"
+        git_dir.mkdir()
+
+        # Test no rebase in progress
+        assert not is_rebase_in_progress(repo_dir)
+
+        # Test rebase-merge directory exists
+        rebase_merge_dir = git_dir / "rebase-merge"
+        rebase_merge_dir.mkdir()
+        assert is_rebase_in_progress(repo_dir)
+
+        # Clean up and test rebase-apply directory
+        rebase_merge_dir.rmdir()
+        assert not is_rebase_in_progress(repo_dir)
+
+        rebase_apply_dir = git_dir / "rebase-apply"
+        rebase_apply_dir.mkdir()
+        assert is_rebase_in_progress(repo_dir)
+
+        # Test both directories exist
+        rebase_merge_dir.mkdir()
+        assert is_rebase_in_progress(repo_dir)
+
+        # Test with None repo_dir (current directory)
+        # This should not raise an error even if .git doesn't exist in cwd
+        assert not is_rebase_in_progress(None)