diff --git a/src/agents/extensions/memory/advanced_sqlite_session.py b/src/agents/extensions/memory/advanced_sqlite_session.py
index 83c289bdf8..3b0a5c0356 100644
--- a/src/agents/extensions/memory/advanced_sqlite_session.py
+++ b/src/agents/extensions/memory/advanced_sqlite_session.py
@@ -786,14 +786,23 @@ def _delete_sync():
 
                     structure_deleted = cursor.rowcount
 
+                    # Drop messages that only this branch referenced. The helper
+                    # is scoped to ``self.session_id`` and removes only rows
+                    # without any ``message_structure`` reference, so it keeps
+                    # messages that the main branch or other branches still
+                    # share via ``_copy_messages_to_new_branch`` (#3346).
+                    orphaned_deleted = self._cleanup_orphaned_messages_sync(conn)
+
                     conn.commit()
 
-                    return usage_deleted, structure_deleted
+                    return usage_deleted, structure_deleted, orphaned_deleted
 
-        usage_deleted, structure_deleted = await asyncio.to_thread(_delete_sync)
+        usage_deleted, structure_deleted, orphaned_deleted = await asyncio.to_thread(_delete_sync)
 
         self._logger.info(
-            f"Deleted branch '{branch_id}': {structure_deleted} message entries, {usage_deleted} usage entries"  # noqa: E501
+            f"Deleted branch '{branch_id}': {structure_deleted} message entries, "
+            f"{orphaned_deleted} orphaned messages, "
+            f"{usage_deleted} usage entries"
         )
 
     async def list_branches(self) -> list[dict[str, Any]]:
diff --git a/tests/extensions/memory/test_advanced_sqlite_session.py b/tests/extensions/memory/test_advanced_sqlite_session.py
index ad4b5c4d86..cf8bd5b602 100644
--- a/tests/extensions/memory/test_advanced_sqlite_session.py
+++ b/tests/extensions/memory/test_advanced_sqlite_session.py
@@ -1422,3 +1422,102 @@ async def test_output_tokens_details_persisted_when_input_details_missing():
     assert turn_usage["output_tokens_details"] == {"reasoning_tokens": 42}
     assert turn_usage["input_tokens_details"] is None
     session.close()
+
+
+async def test_delete_branch_cleans_branch_only_messages():
+    """delete_branch must drop messages that were only referenced by that branch.
+
+    Regression test for https://github.com/openai/openai-agents-python/issues/3346.
+    Previously ``delete_branch`` removed ``turn_usage`` and ``message_structure``
+    rows for the deleted branch but left the underlying ``agent_messages`` rows
+    in the table when no other branch still referenced them. After this fix the
+    orphaned rows are cleaned up while messages still shared with main or other
+    branches are preserved.
+    """
+    session_id = "delete_branch_orphan_test"
+    session = AdvancedSQLiteSession(session_id=session_id, create_tables=True)
+
+    # Two messages on main, then a branch-only pair that only the branch sees.
+    await session.add_items(
+        [
+            {"role": "user", "content": "main question"},
+            {"role": "assistant", "content": "main answer"},
+        ]
+    )
+
+    await session.create_branch_from_turn(1, "branch_only")
+    await session.add_items(
+        [
+            {"role": "user", "content": "branch-only question"},
+            {"role": "assistant", "content": "branch-only answer"},
+        ]
+    )
+
+    await session.delete_branch("branch_only", force=True)
+
+    # After deletion only the two main-branch messages should remain in the
+    # base ``agent_messages`` table; ``message_structure`` should only have the
+    # main-branch references.
+    with session._locked_connection() as conn:
+        message_rows = conn.execute(
+            f"""
+            SELECT id, message_data
+            FROM {session.messages_table}
+            WHERE session_id = ?
+            ORDER BY id
+            """,
+            (session.session_id,),
+        ).fetchall()
+        structure_rows = conn.execute(
+            """
+            SELECT branch_id, message_id
+            FROM message_structure
+            WHERE session_id = ?
+            ORDER BY message_id
+            """,
+            (session.session_id,),
+        ).fetchall()
+
+    message_contents = [json.loads(row[1]).get("content") for row in message_rows]
+    assert message_contents == ["main question", "main answer"]
+
+    branch_ids = {row[0] for row in structure_rows}
+    assert branch_ids == {"main"}
+
+    session.close()
+
+
+async def test_delete_branch_preserves_messages_shared_with_main():
+    """delete_branch must keep messages that the main branch still references."""
+    session_id = "delete_branch_shared_test"
+    session = AdvancedSQLiteSession(session_id=session_id, create_tables=True)
+
+    # Two user-led turns on main so a branch can fork at turn 2 while still
+    # sharing turn 1's messages.
+    await session.add_items(
+        [
+            {"role": "user", "content": "main question"},
+            {"role": "assistant", "content": "main answer"},
+        ]
+    )
+    await session.add_items(
+        [
+            {"role": "user", "content": "main follow-up"},
+            {"role": "assistant", "content": "main follow-up answer"},
+        ]
+    )
+
+    await session.create_branch_from_turn(2, "experiment")
+
+    # Delete the branch. Messages still referenced by main must stay.
+    await session.delete_branch("experiment", force=True)
+
+    main_items = await session.get_items()
+    assert [item.get("content") for item in main_items] == [
+        "main question",
+        "main answer",
+        "main follow-up",
+        "main follow-up answer",
+    ]
+
+    session.close()