diff --git a/monai/apps/auto3dseg/auto_runner.py b/monai/apps/auto3dseg/auto_runner.py
index 37ccf7f19d..989ac71451 100644
--- a/monai/apps/auto3dseg/auto_runner.py
+++ b/monai/apps/auto3dseg/auto_runner.py
@@ -202,7 +202,7 @@ class AutoRunner:
 
         For the datalist file format, see the description under :py:func:`monai.data.load_decathlon_datalist`.
         Note that the AutoRunner will use the "validation" key in the datalist file if it exists, otherwise
-        it will do cross-validation, by default with five folds (this is hardcoded).
+        it will do cross-validation with the configured num_fold (five folds by default).
     """
 
     analyze_params: dict | None
@@ -399,7 +399,7 @@ def inspect_datalist_folds(self, datalist_filename: str) -> int:
             datalist_filename: path to the datalist file.
 
         Notes:
-            If the fold key is not provided, it auto generates 5 folds assignments in the training key list.
+            If the fold key is not provided, it generates the configured num_fold assignments (default 5).
             If validation key list is available, then it assumes a single fold validation.
         """
 
@@ -440,7 +440,7 @@ def inspect_datalist_folds(self, datalist_filename: str) -> int:
             num_fold = 1
 
         else:
-            num_fold = 5
+            num_fold = int(self.data_src_cfg.get("num_fold", 5))
 
             warnings.warn(
                 f"Datalist has no folds specified {datalist_filename}..."
diff --git a/tests/apps/test_auto_runner_num_fold.py b/tests/apps/test_auto_runner_num_fold.py
new file mode 100644
index 0000000000..37e7cd5b35
--- /dev/null
+++ b/tests/apps/test_auto_runner_num_fold.py
@@ -0,0 +1,98 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import json
+import logging
+import tempfile
+import unittest
+from pathlib import Path
+
+from parameterized import parameterized
+
+from monai.apps.auto3dseg import AutoRunner
+from monai.utils import optional_import
+
+_, has_sklearn = optional_import("sklearn.model_selection", name="KFold")
+_, has_yaml = optional_import("yaml")
+
+
+@unittest.skipUnless(has_sklearn and has_yaml, "scikit-learn and PyYAML required")
+class TestAutoRunnerNumFold(unittest.TestCase):
+    def setUp(self):
+        temp_dir = tempfile.TemporaryDirectory()
+        self.addCleanup(temp_dir.cleanup)
+        self.tmp_path = Path(temp_dir.name)
+
+    def test_autorunner_generates_configured_num_fold(self):
+        tmp_path = self.tmp_path
+        datalist_path = tmp_path / "datalist.json"
+        datalist_path.write_text(
+            json.dumps({"training": [{"image": f"image_{i}.nii.gz", "label": f"label_{i}.nii.gz"} for i in range(10)]}),
+            encoding="utf-8",
+        )
+        runner = AutoRunner(
+            work_dir=str(tmp_path / "work"),
+            input={"modality": "CT", "dataroot": str(tmp_path), "datalist": str(datalist_path), "num_fold": 2},
+            analyze=False,
+            algo_gen=False,
+            train=False,
+            ensemble=False,
+        )
+        with open(runner.datalist_filename, encoding="utf-8") as f:
+            generated = json.load(f)
+
+        assert runner.num_fold == 2
+        assert {item["fold"] for item in generated["training"]} == {0, 1}
+
+    @parameterized.expand([("default",), ("existing_folds",), ("validation",), ("six_folds",)])
+    def test_autorunner_fold_compatibility(self, case):
+        tmp_path = self.tmp_path
+        training = [{"image": f"image_{i}.nii.gz", "label": f"label_{i}.nii.gz"} for i in range(10)]
+        datalist = {"training": training}
+        datalist_path = tmp_path / "datalist.json"
+        config = {"modality": "CT", "dataroot": str(tmp_path), "datalist": str(datalist_path)}
+        expected_training = None
+        expected_num_fold = 5
+
+        if case == "existing_folds":
+            for i, item in enumerate(training):
+                item["fold"] = i % 5
+            config["num_fold"] = expected_num_fold = 2
+            expected_training = training
+        elif case == "validation":
+            # Avoid an existing malformed INFO message in the validation merge path.
+            logger = logging.getLogger("monai.apps.auto3dseg.auto_runner")
+            self.addCleanup(logger.setLevel, logger.level)
+            logger.setLevel(logging.WARNING)
+            # Include an overlapping case and a validation-only case to check merging.
+            datalist["validation"] = [training[0].copy(), {"image": "val.nii.gz", "label": "val_label.nii.gz"}]
+            config["num_fold"] = expected_num_fold = 1
+            expected_training = [dict(item, fold=0 if i == 0 else 1) for i, item in enumerate(training)]
+            expected_training.append(dict(datalist["validation"][1], fold=0))
+        elif case == "six_folds":
+            config["num_fold"] = expected_num_fold = 6
+
+        datalist_path.write_text(json.dumps(datalist), encoding="utf-8")
+        runner = AutoRunner(
+            work_dir=str(tmp_path / "work"), input=config, analyze=False, algo_gen=False, train=False, ensemble=False
+        )
+        with open(runner.datalist_filename, encoding="utf-8") as f:
+            generated = json.load(f)
+
+        assert runner.num_fold == expected_num_fold
+        if expected_training is not None:
+            assert generated["training"] == expected_training
+        else:
+            assert len(generated["training"]) == 10
+            assert {item["fold"] for item in generated["training"]} == set(range(expected_num_fold))
+        assert json.loads(datalist_path.read_text(encoding="utf-8")) == datalist