diff --git a/payu/fsops.py b/payu/fsops.py
index 6560eade..0ff2b286 100644
--- a/payu/fsops.py
+++ b/payu/fsops.py
@@ -301,6 +301,18 @@ def needs_subprocess_shell(command: str) -> bool:
     return False
 
 
+def env_with_python_path():
+    """Return a copy of current environment variables with PATH
+    modified to include the python interpreter"""
+    # Get the directory of the current Python interpreter
+    python_dir = os.path.dirname(sys.executable)
+
+    # Add Python interpreter to PATH
+    env = os.environ.copy()
+    env["PATH"] = python_dir + os.pathsep + env["PATH"]
+    return env
+
+
 def _run_script(script_cmd: str, control_path: Path) -> None:
     """Helper recursive function to attempt running a script command.
 
@@ -315,9 +327,11 @@ def _run_script(script_cmd: str, control_path: Path) -> None:
     # First try to interpret the argument as a full command
     try:
         if needs_subprocess_shell(script_cmd):
-            subprocess.check_call(script_cmd, shell=True)
+            subprocess.check_call(script_cmd, shell=True,
+                                  env=env_with_python_path())
         else:
-            subprocess.check_call(shlex.split(script_cmd))
+            subprocess.check_call(shlex.split(script_cmd),
+                                  env=env_with_python_path())
         print(script_cmd)
 
     except FileNotFoundError:
diff --git a/test/test_payu.py b/test/test_payu.py
index 7ab218cf..a0416b32 100644
--- a/test/test_payu.py
+++ b/test/test_payu.py
@@ -6,6 +6,7 @@
 import shutil
 import stat
 import sys
+from unittest.mock import patch
 
 # Submodules
 import payu
@@ -327,20 +328,22 @@ def test_run_userscript_python_script_with_shebang_header(tmp_path):
     with open(python_script, 'w') as f:
         f.writelines([
             '#!/usr/bin/env python\n'
+            'import sys\n'
             f"with open('{tmp_path}/output.txt', 'w') as f:\n",
-            "   f.write('Test Python user script with python shebang header')"
+            "   f.write(f'{sys.executable}')"
         ])
 
     # Make file executable
     os.chmod(python_script, 0o775)
 
     # Test run userscript
-    payu.fsops.run_script_command('test_script_with_python_shebang.py',
-                                  tmp_path)
+    with patch.dict(os.environ, {'PATH': '/mocked/path'}):
+        payu.fsops.run_script_command('test_script_with_python_shebang.py',
+                                      tmp_path)
 
-    # Check script output
+    # Check script is run with same python executable as caller
     with open((tmp_path / 'output.txt'), 'r') as f:
-        assert f.read() == "Test Python user script with python shebang header"
+        assert sys.executable.startswith(f.read())
 
 
 def test_run_userscript_bash_script(tmp_path):