diff --git a/api/services/dataset_service.py b/api/services/dataset_service.py
index fe36c270496..8b3464bf5ae 100644
--- a/api/services/dataset_service.py
+++ b/api/services/dataset_service.py
@@ -2341,6 +2341,23 @@ class DocumentService:
                         if not knowledge_config.data_source.info_list.file_info_list:
                             raise ValueError("File source info is required")
                         upload_file_list = knowledge_config.data_source.info_list.file_info_list.file_ids
+                        # Issue #41735: under MySQL's default
+                        # ``REPEATABLE READ`` isolation, the SELECT snapshot
+                        # for this transaction is pinned by the first
+                        # read done earlier in ``save_document_with_dataset_id``
+                        # (e.g. ``check_doc_form``). The caller has just
+                        # committed the upload in a different session
+                        # (``FileService.upload_text`` /
+                        # ``FileService.upload_file``), so the rows exist
+                        # but are invisible to *this* session until its
+                        # snapshot is refreshed. End the current transaction
+                        # so the next SELECT starts with a fresh snapshot.
+                        # The pending changes on ``dataset`` are also
+                        # flushed, which is what we want — they must be
+                        # persisted by this point anyway. PostgreSQL's
+                        # default ``READ COMMITTED`` rebuilds the read view
+                        # per statement so it isn't affected.
+                        session.commit()
                         files = list(
                             session.scalars(
                                 select(UploadFile).where(
diff --git a/api/tests/unit_tests/services/dataset_service/test_save_document_with_dataset_id_mysql_snapshot.py b/api/tests/unit_tests/services/dataset_service/test_save_document_with_dataset_id_mysql_snapshot.py
new file mode 100644
index 00000000000..e8af9b89ca1
--- /dev/null
+++ b/api/tests/unit_tests/services/dataset_service/test_save_document_with_dataset_id_mysql_snapshot.py
@@ -0,0 +1,70 @@
+"""Regression coverage for #41735.
+
+The pre-fix code in ``DocumentService.save_document_with_dataset_id``
+read ``UploadFile`` rows inside a single session that had its
+``REPEATABLE READ`` snapshot pinned by an earlier ``Dataset`` SELECT.
+When ``FileService.upload_text`` / ``upload_file`` committed the
+``upload_files`` row in a SEPARATE session, the row was invisible to
+*this* session until the snapshot was refreshed, and
+``save_document_with_dataset_id`` reported ``One or more files not
+found.`` even though the row was committed (verified via a second
+session).
+
+The fix forces ``session.commit()`` immediately before the
+``UploadFile`` lookup so the next SELECT starts a fresh snapshot.
+This file pins that contract by reading the function source and
+asserting the structural invariant directly.
+"""
+
+from __future__ import annotations
+
+import inspect
+
+from services.dataset_service import DocumentService
+
+
+def test_session_committed_before_upload_file_lookup() -> None:
+    """#41735: ``session.commit()`` must run BEFORE the ``UploadFile``
+    SELECT so the SELECT sees rows committed by ``FileService.upload_text``
+    on a different session. MySQL REPEATABLE READ keeps the original
+    snapshot for the rest of the transaction; the commit ends it so the
+    next SELECT starts a fresh transaction with a new snapshot.
+    PostgreSQL's default READ COMMITTED rebuilds the read view per
+    statement so the extra commit is a no-op there.
+
+    Read the function source and assert that ``session.commit()`` is
+    called BEFORE the ``UploadFile`` SELECT — the same structural
+    invariant the reproduction in the issue depends on, without needing
+    a live MySQL database.
+    """
+    source_lines = inspect.getsource(DocumentService.save_document_with_dataset_id).splitlines()
+
+    upload_select_line = next(
+        (i for i, line in enumerate(source_lines) if "select(UploadFile)" in line),
+        None,
+    )
+    assert upload_select_line is not None, "save_document_with_dataset_id must contain a select(UploadFile) call"
+
+    # Find every ``session.commit()`` call, then keep the last one
+    # whose line number is BEFORE the UploadFile SELECT. If the fix is
+    # in place, that commit is the snapshot refresh.
+    last_commit_before_upload = -1
+    for i, line in enumerate(source_lines):
+        if i >= upload_select_line:
+            break
+        if "session.commit()" in line:
+            last_commit_before_upload = i
+
+    assert last_commit_before_upload >= 0, (
+        "save_document_with_dataset_id must call session.commit() at least once before the UploadFile SELECT"
+    )
+
+    # The fix is a focused call: one extra ``session.commit()`` between
+    # the (already-existing) ``DocumentService.check_doc_form`` call and
+    # the ``select(UploadFile)`` call. Pin that there's a comment
+    # referencing #41735 right above the new commit so a future edit
+    # doesn't accidentally delete the snapshot refresh without
+    # understanding why it's there.
+    assert "#41735" in "\n".join(source_lines), (
+        "The fix's invariant comment referencing issue #41735 must be present in save_document_with_dataset_id"
+    )