diff --git a/src/agents/extensions/memory/advanced_sqlite_session.py b/src/agents/extensions/memory/advanced_sqlite_session.py
index 83c289bdf8..38ad5b32dd 100644
--- a/src/agents/extensions/memory/advanced_sqlite_session.py
+++ b/src/agents/extensions/memory/advanced_sqlite_session.py
@@ -786,14 +786,21 @@ def _delete_sync():
 
                     structure_deleted = cursor.rowcount
 
+                    # Drop any base messages that this branch was the only
+                    # reference for. Without this step, branch-only rows become
+                    # invisible to advanced reads (which join through
+                    # `message_structure`) but linger in the base table.
+                    orphans_deleted = self._cleanup_orphaned_messages_sync(conn)
+
                     conn.commit()
 
-                    return usage_deleted, structure_deleted
+                    return usage_deleted, structure_deleted, orphans_deleted
 
-        usage_deleted, structure_deleted = await asyncio.to_thread(_delete_sync)
+        usage_deleted, structure_deleted, orphans_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"{usage_deleted} usage entries, {orphans_deleted} orphaned base rows"
         )
 
     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..9b874179f2 100644
--- a/tests/extensions/memory/test_advanced_sqlite_session.py
+++ b/tests/extensions/memory/test_advanced_sqlite_session.py
@@ -1422,3 +1422,60 @@ 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_removes_branch_only_base_messages():
+    """Regression for #3346.
+
+    `delete_branch` used to remove only the `turn_usage` and `message_structure`
+    rows for a branch, leaving the underlying messages in the base table when
+    they were only referenced by that branch. Those rows became invisible to
+    advanced reads (which join through `message_structure`) but still padded
+    the on-disk database. After the fix, branch-only messages are dropped along
+    with their structure rows, while messages shared with another branch are
+    preserved.
+    """
+    session = AdvancedSQLiteSession(
+        session_id="delete_branch_orphan_repro",
+        create_tables=True,
+    )
+
+    try:
+        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)
+
+        with session._locked_connection() as conn:
+            message_rows = conn.execute(
+                f"SELECT id FROM {session.messages_table} WHERE session_id = ? ORDER BY id",
+                (session.session_id,),
+            ).fetchall()
+            structure_rows = conn.execute(
+                "SELECT branch_id FROM message_structure WHERE session_id = ?",
+                (session.session_id,),
+            ).fetchall()
+
+        # Main-branch messages remain (shared between branches were copied at
+        # `create_branch_from_turn`, so the two new branch-only rows were the
+        # only references for ids 3 and 4 — both should be gone now).
+        assert [row[0] for row in message_rows] == [1, 2]
+        assert all(row[0] == "main" for row in structure_rows)
+        assert await session.get_items(branch_id="main") == [
+            {"role": "user", "content": "main question"},
+            {"role": "assistant", "content": "main answer"},
+        ]
+    finally:
+        session.close()