diff --git a/checkpoint/orbax/checkpoint/experimental/v1/_src/partial/run_merging.py b/checkpoint/orbax/checkpoint/experimental/v1/_src/partial/run_merging.py
new file mode 100644
index 000000000..196bac92f
--- /dev/null
+++ b/checkpoint/orbax/checkpoint/experimental/v1/_src/partial/run_merging.py
@@ -0,0 +1,97 @@
+# Copyright 2026 The Orbax Authors.
+#
+# 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.
+
+"""Merging utility for Orbax checkpoints."""
+
+import asyncio
+from collections.abc import Sequence
+
+from absl import app
+from absl import flags
+from etils import epath
+import jax
+from orbax.checkpoint.experimental.v1._src.layout import orbax_layout
+from orbax.checkpoint.experimental.v1._src.partial import merging
+
+
+FLAGS = flags.FLAGS
+
+_IN_PATHS = flags.DEFINE_multi_string(
+    'in_paths',
+    None,
+    'Paths of checkpoints to merge.',
+)
+_OUT_PATH = flags.DEFINE_string(
+    'out_path',
+    None,
+    'Output checkpoint path.',
+)
+_PER_HOST_MEMORY_LIMIT_BYTES = flags.DEFINE_integer(
+    'per_host_memory_limit_bytes',
+    None,
+    'Memory limit in bytes per CPU host for partial loading and saving.'
+    ' Non-uniform memory limits are not supported.',
+)
+
+
+def main(argv: Sequence[str]) -> None:
+  if len(argv) > 1:
+    raise app.UsageError('Too many command-line arguments.')
+
+  if not _IN_PATHS.value:
+    raise app.UsageError('Flag --in_paths must be specified.')
+  if _OUT_PATH.value is None:
+    raise app.UsageError('Flag --out_path must be specified.')
+  if _PER_HOST_MEMORY_LIMIT_BYTES.value is None:
+    raise app.UsageError(
+        'Flag --per_host_memory_limit_bytes must be specified.'
+    )
+
+  if _PER_HOST_MEMORY_LIMIT_BYTES.value <= 0:
+    raise ValueError('per_host_memory_limit_bytes must be positive.')
+
+  # Validate input checkpoints.
+  layout = orbax_layout.OrbaxLayout()
+  for path_str in _IN_PATHS.value:
+    path = epath.Path(path_str)
+    if not path.exists():
+      raise FileNotFoundError(f'Input path {path_str} does not exist.')
+    # OrbaxLayout.validate is async.
+    try:
+      asyncio.run(layout.validate(path))
+    except Exception as e:
+      raise ValueError(
+          f'Input path {path_str} is not a valid checkpoint.'
+      ) from e
+
+  # Validate output path.
+  out_path = epath.Path(_OUT_PATH.value)
+  if out_path.exists():
+    if not out_path.is_dir():
+      raise ValueError(
+          f'Output path {_OUT_PATH.value} exists but is not a directory.'
+      )
+    if list(out_path.iterdir()):
+      raise ValueError(
+          f'Output path {_OUT_PATH.value} exists and is not empty.'
+      )
+
+  if jax.process_index() == 0:
+    out_path.mkdir(parents=True, exist_ok=True)
+
+  merging.merge_checkpoints(
+      _IN_PATHS.value,
+      _OUT_PATH.value,
+      _PER_HOST_MEMORY_LIMIT_BYTES.value,
+  )
diff --git a/checkpoint/orbax/checkpoint/experimental/v1/_src/partial/run_merging_test.py b/checkpoint/orbax/checkpoint/experimental/v1/_src/partial/run_merging_test.py
new file mode 100644
index 000000000..9ccf596ae
--- /dev/null
+++ b/checkpoint/orbax/checkpoint/experimental/v1/_src/partial/run_merging_test.py
@@ -0,0 +1,82 @@
+# Copyright 2026 The Orbax Authors.
+#
+# 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 unittest import mock
+
+from absl.testing import absltest
+from absl.testing import flagsaver
+from etils import epath
+import jax
+from orbax.checkpoint.experimental.v1._src.layout import orbax_layout
+from orbax.checkpoint.experimental.v1._src.partial import merging
+from orbax.checkpoint.experimental.v1._src.partial import run_merging
+
+
+class RunMergingTest(absltest.TestCase):
+
+  def setUp(self):
+    super().setUp()
+    self.out_path = self.create_tempdir().full_path
+    self.in_paths = [self.create_tempdir().full_path]
+
+  @mock.patch.object(
+      orbax_layout.OrbaxLayout, 'validate', new_callable=mock.AsyncMock
+  )
+  @mock.patch.object(merging, 'merge_checkpoints', autospec=True)
+  @mock.patch.object(jax, 'process_index', return_value=0)
+  def test_main_success(self, _, mock_merge, mock_validate):
+    with flagsaver.flagsaver(
+        in_paths=self.in_paths,
+        out_path=self.out_path,
+        per_host_memory_limit_bytes=1024,
+    ):
+      run_merging.main([])
+
+    mock_validate.assert_called()
+    mock_merge.assert_called_once()
+
+  @mock.patch.object(
+      orbax_layout.OrbaxLayout, 'validate', new_callable=mock.AsyncMock
+  )
+  @mock.patch.object(jax, 'process_index', return_value=0)
+  def test_main_invalid_output_not_empty(self, *_):
+    out_path = epath.Path(self.out_path)
+    (out_path / 'some_file').write_text('content')
+
+    with flagsaver.flagsaver(
+        in_paths=self.in_paths,
+        out_path=self.out_path,
+        per_host_memory_limit_bytes=1024,
+    ):
+      with self.assertRaisesRegex(ValueError, 'not empty'):
+        run_merging.main([])
+
+  @mock.patch.object(
+      orbax_layout.OrbaxLayout, 'validate', new_callable=mock.AsyncMock
+  )
+  @mock.patch.object(jax, 'process_index', return_value=0)
+  def test_main_invalid_input(self, _, mock_validate):
+    mock_validate.side_effect = ValueError('Invalid checkpoint')
+
+    with flagsaver.flagsaver(
+        in_paths=self.in_paths,
+        out_path=self.out_path,
+        per_host_memory_limit_bytes=1024,
+    ):
+      with self.assertRaisesRegex(ValueError, 'is not a valid checkpoint'):
+        run_merging.main([])
+
+
+if __name__ == '__main__':
+  absltest.main()