diff --git a/codeflash/benchmarking/compare.py b/codeflash/benchmarking/compare.py
index 9ce4db01b..237753cb8 100644
--- a/codeflash/benchmarking/compare.py
+++ b/codeflash/benchmarking/compare.py
@@ -211,6 +211,7 @@ def compare_branches(
     functions: Optional[dict[Path, list[FunctionToOptimize]]] = None,
     timeout: int = 600,
     memory: bool = False,
+    inject_paths: Optional[list[str]] = None,
 ) -> CompareResult:
     """Compare benchmark performance between two git refs.
 
@@ -343,6 +344,24 @@ def build_panel(current_step: int) -> Panel:
             head_sha = repo.commit(head_ref).hexsha
             repo.git.worktree("add", str(base_worktree), base_sha)
             repo.git.worktree("add", str(head_worktree), head_sha)
+
+            # Inject files from working tree into both worktrees
+            if inject_paths:
+                import shutil
+
+                for path_str in inject_paths:
+                    src = repo_root / path_str
+                    if not src.exists():
+                        logger.warning("Inject path does not exist: %s", src)
+                        continue
+                    for wt in [base_worktree, head_worktree]:
+                        dst = wt / path_str
+                        dst.parent.mkdir(parents=True, exist_ok=True)
+                        if src.is_dir():
+                            shutil.copytree(src, dst, dirs_exist_ok=True)
+                        elif src.is_file():
+                            shutil.copy2(src, dst)
+
             step += 1
             live.update(build_panel(step))
 
diff --git a/codeflash/cli_cmds/cli.py b/codeflash/cli_cmds/cli.py
index cf5ca7bdd..954a1165d 100644
--- a/codeflash/cli_cmds/cli.py
+++ b/codeflash/cli_cmds/cli.py
@@ -403,6 +403,12 @@ def _build_parser() -> ArgumentParser:
         help="Relative path to JSON results file produced by --script (required with --script)",
     )
     compare_parser.add_argument("--config-file", type=str, dest="config_file", help="Path to pyproject.toml")
+    compare_parser.add_argument(
+        "--inject",
+        nargs="+",
+        default=None,
+        help="Files or directories to copy into both worktrees before benchmarking. Paths are relative to repo root.",
+    )
 
     trace_optimize = subparsers.add_parser("optimize", help="Trace and optimize your project.")
 
diff --git a/codeflash/cli_cmds/cmd_compare.py b/codeflash/cli_cmds/cmd_compare.py
index 898af5679..87d659fdb 100644
--- a/codeflash/cli_cmds/cmd_compare.py
+++ b/codeflash/cli_cmds/cmd_compare.py
@@ -40,6 +40,9 @@ def run_compare(args: Namespace) -> None:
     # Script mode: run an arbitrary benchmark command on each worktree (no codeflash config needed)
     script_cmd = getattr(args, "script", None)
     if script_cmd:
+        if getattr(args, "inject", None):
+            logger.warning("--inject is not supported in --script mode and will be ignored")
+
         script_output = getattr(args, "script_output", None)
         if not script_output:
             logger.error("--script-output is required when using --script")
@@ -108,6 +111,7 @@ def run_compare(args: Namespace) -> None:
         functions=functions,
         timeout=args.timeout,
         memory=getattr(args, "memory", False),
+        inject_paths=getattr(args, "inject", None),
     )
 
     if not result.base_stats and not result.head_stats: