diff --git a/flepimop/gempyor_pkg/src/gempyor/batch.py b/flepimop/gempyor_pkg/src/gempyor/batch.py
index 2510dfc33..7fccea7c9 100644
--- a/flepimop/gempyor_pkg/src/gempyor/batch.py
+++ b/flepimop/gempyor_pkg/src/gempyor/batch.py
@@ -29,7 +29,7 @@
 from .file_paths import run_id
 from .info import Cluster, get_cluster_info
 from .logging import get_script_logger
-from .utils import _format_cli_options, _git_head, _shutil_which, config
+from .utils import _format_cli_options, _git_checkout, _git_head, _shutil_which, config
 from .shared_cli import (
     NONNEGATIVE_DURATION,
     cli,
@@ -981,6 +981,13 @@ def _submit_scenario_job(
             default=False,
             help="Flag to reset chimerics on global accept.",
         ),
+        click.Option(
+            param_decls=["--skip-checkout", "skip_checkout"],
+            type=bool,
+            default=False,
+            is_flag=True,
+            help="Flag to skip checking out a new branch in the project git directory.",
+        ),
     ]
     + list(verbosity_options.values()),
 )
@@ -1123,3 +1130,15 @@ def _click_submit(ctx: click.Context = mock_context, **kwargs: Any) -> None:
             kwargs["dry_run"],
             now,
         )
+
+    # Checkout a new branch to preserve run information
+    if kwargs["skip_checkout"]:
+        logger.debug("Skipped checking out a new branch to preserve run.")
+    else:
+        branch = f"run_{job_name}"
+        _git_checkout(kwargs["project_path"], branch)
+        logger.info(
+            "Checked out a new branch, '%s', in the project "
+            "repository to preserve run details.",
+            branch,
+        )
diff --git a/flepimop/gempyor_pkg/src/gempyor/utils.py b/flepimop/gempyor_pkg/src/gempyor/utils.py
index 20ed5de58..5b9b75fa1 100644
--- a/flepimop/gempyor_pkg/src/gempyor/utils.py
+++ b/flepimop/gempyor_pkg/src/gempyor/utils.py
@@ -1118,6 +1118,29 @@ def _git_head(repository: Path) -> str:
     return proc.stdout.decode().strip()
 
 
+def _git_checkout(repository: Path, branch: str) -> None:
+    """
+    Checkout a new branch from a given git repository.
+
+    Args:
+        repository: A directory under version control with git to
+            checkout a new branch in.
+        branch: The name of the new branch to checkout.
+
+    Examples:
+        >>> from pathlib import Path
+        >>> _git_checkout(Path("~/Desktop/GitHub/HopkinsIDD/flepiMoP"), "my-new-branch")
+    """
+    git_cmd = _shutil_which("git")
+    subprocess.run(
+        [git_cmd, "checkout", "-b", branch],
+        cwd=repository.expanduser().absolute(),
+        check=True,
+        stdout=subprocess.DEVNULL,
+        stderr=subprocess.DEVNULL,
+    )
+
+
 def _format_cli_options(options: dict[str, Any]) -> list[str]:
     """
     Convert a dictionary of CLI options into a formatted list.