diff --git a/src/claude_agent_sdk/_internal/sessions.py b/src/claude_agent_sdk/_internal/sessions.py
index 2634a0f37..21a72bb63 100644
--- a/src/claude_agent_sdk/_internal/sessions.py
+++ b/src/claude_agent_sdk/_internal/sessions.py
@@ -1299,9 +1299,9 @@ def list_subagents(
             searches all project directories under ``~/.claude/projects/``.
 
     Returns:
-        List of subagent ID strings. Returns an empty list if the session
-        is not found, the session_id is not a valid UUID, or the session
-        has no subagents.
+        List of unique subagent ID strings in discovery order. Returns an
+        empty list if the session is not found, the session_id is not a valid
+        UUID, or the session has no subagents.
 
     See Also:
         :func:`list_subagents_from_store` for the :class:`SessionStore`-backed
@@ -1322,7 +1322,9 @@ def list_subagents(
     if subagents_dir is None:
         return []
 
-    return [agent_id for agent_id, _ in _collect_agent_files(subagents_dir)]
+    return list(
+        dict.fromkeys(agent_id for agent_id, _ in _collect_agent_files(subagents_dir))
+    )
 
 
 def get_subagent_messages(
diff --git a/tests/test_sessions.py b/tests/test_sessions.py
index 3e2ffd9a4..987610fe2 100644
--- a/tests/test_sessions.py
+++ b/tests/test_sessions.py
@@ -1715,6 +1715,22 @@ def test_recurses_into_subdirectories(
         result = list_subagents(sid, directory=project_path)
         assert sorted(result) == ["nested", "top"]
 
+    def test_dedupes_agent_id_across_subdirectories(
+        self, claude_config_dir: Path, tmp_path: Path
+    ):
+        """Duplicate IDs are returned once in their first-seen order."""
+        project_path = str(tmp_path / "proj")
+        Path(project_path).mkdir(parents=True)
+        sid, subagents_dir = _make_session_with_subagents(
+            claude_config_dir, project_path, agent_ids=["top"]
+        )
+        nested = subagents_dir / "workflows" / "run-1"
+        nested.mkdir(parents=True)
+        (nested / "agent-nested.jsonl").write_text("{}\n")
+        (nested / "agent-top.jsonl").write_text("{}\n")
+
+        assert list_subagents(sid, directory=project_path) == ["top", "nested"]
+
     def test_searches_all_projects_without_directory(self, claude_config_dir: Path):
         """When directory is omitted, all project directories are searched."""
         project_dir = _make_project_dir(claude_config_dir, "/some/project")