diff --git a/.semversioner/next-release/patch-20260705142108838934.json b/.semversioner/next-release/patch-20260705142108838934.json
new file mode 100644
index 000000000..a5291f0f2
--- /dev/null
+++ b/.semversioner/next-release/patch-20260705142108838934.json
@@ -0,0 +1,4 @@
+{
+  "type": "patch",
+  "description": "Ignore blank lines when loading JSONL input files."
+}
diff --git a/packages/graphrag-input/graphrag_input/jsonl.py b/packages/graphrag-input/graphrag_input/jsonl.py
index f038aafaa..cea9d6b27 100644
--- a/packages/graphrag-input/graphrag_input/jsonl.py
+++ b/packages/graphrag-input/graphrag_input/jsonl.py
@@ -34,5 +34,5 @@ async def read_file(self, path: str) -> list[TextDocument]:
             - output - list with a TextDocument for each row in the file.
         """
         text = await self._storage.get(path, encoding=self._encoding)
-        rows = [json.loads(line) for line in text.splitlines()]
+        rows = [json.loads(line) for line in text.splitlines() if line.strip()]
         return await self.process_data_columns(rows, path)
diff --git a/tests/unit/indexing/input/test_jsonl_loader.py b/tests/unit/indexing/input/test_jsonl_loader.py
index dd5609429..80aea5afe 100644
--- a/tests/unit/indexing/input/test_jsonl_loader.py
+++ b/tests/unit/indexing/input/test_jsonl_loader.py
@@ -40,3 +40,24 @@ async def test_jsonl_loader_one_file_with_title():
     documents = await reader.read_files()
     assert len(documents) == 3
     assert documents[0].title == "Hello"
+
+
+async def test_jsonl_loader_ignores_blank_lines(tmp_path):
+    (tmp_path / "input.jsonl").write_text(
+        '{"title":"Hello","text":"Hi"}\n\n   \n{"title":"Goodbye","text":"Bye"}\n',
+        encoding="utf-8",
+    )
+    config = InputConfig(
+        type=InputType.JsonLines,
+        title_column="title",
+    )
+    storage = create_storage(
+        StorageConfig(
+            base_dir=str(tmp_path),
+        )
+    )
+    reader = create_input_reader(config, storage)
+    documents = await reader.read_files()
+    assert len(documents) == 2
+    assert [doc.title for doc in documents] == ["Hello", "Goodbye"]
+    assert [doc.text for doc in documents] == ["Hi", "Bye"]