diff --git a/backend/packages/harness/deerflow/config/database_config.py b/backend/packages/harness/deerflow/config/database_config.py
index 19fb297b0..37cfd579d 100644
--- a/backend/packages/harness/deerflow/config/database_config.py
+++ b/backend/packages/harness/deerflow/config/database_config.py
@@ -7,10 +7,9 @@ configures one backend; the system handles physical separation details.
 SQLite mode: checkpointer and app share a single .db file
 ({sqlite_dir}/deerflow.db) with WAL journal mode enabled on every
 connection. WAL allows concurrent readers and a single writer without
-blocking, making a unified file safe for both workloads.  The
-``busy_timeout`` PRAGMA (set in ``engine.py``) ensures writers wait
-for each other instead of failing immediately when they contend for
-the write lock.
+blocking, making a unified file safe for both workloads.  Writers
+that contend for the lock wait via the default 5-second sqlite3
+busy timeout rather than failing immediately.
 
 Postgres mode: both use the same database URL but maintain independent
 connection pools with different lifecycles.
diff --git a/backend/packages/harness/deerflow/persistence/engine.py b/backend/packages/harness/deerflow/persistence/engine.py
index 4857c13a0..2777c2450 100644
--- a/backend/packages/harness/deerflow/persistence/engine.py
+++ b/backend/packages/harness/deerflow/persistence/engine.py
@@ -98,6 +98,11 @@ async def init_engine(
         # SQLite deployment (TC-UPG-06 in AUTH_TEST_PLAN.md). The companion
         # ``synchronous=NORMAL`` is the safe-and-fast pairing — fsync only
         # at WAL checkpoint boundaries instead of every commit.
+        # Note: we do not set PRAGMA busy_timeout here — Python's sqlite3
+        # driver already defaults to a 5-second busy timeout (see the
+        # ``timeout`` kwarg of ``sqlite3.connect``), and aiosqlite /
+        # SQLAlchemy's aiosqlite dialect inherit that default.  Setting
+        # it again would be a no-op.
         @event.listens_for(_engine.sync_engine, "connect")
         def _enable_sqlite_wal(dbapi_conn, _record):  # noqa: ARG001 — SQLAlchemy contract
             cursor = dbapi_conn.cursor()
@@ -105,7 +110,6 @@ async def init_engine(
                 cursor.execute("PRAGMA journal_mode=WAL;")
                 cursor.execute("PRAGMA synchronous=NORMAL;")
                 cursor.execute("PRAGMA foreign_keys=ON;")
-                cursor.execute("PRAGMA busy_timeout=5000;")
             finally:
                 cursor.close()
     elif backend == "postgres":