diff --git a/artiq/tools.py b/artiq/tools.py
index f7a399db7..679293143 100644
--- a/artiq/tools.py
+++ b/artiq/tools.py
@@ -6,6 +6,7 @@ import collections
 import atexit
 import string
 import os
+from copy import copy
 
 import numpy as np
 
@@ -84,8 +85,12 @@ def file_import(filename, prefix="file_import_"):
     path = os.path.dirname(os.path.realpath(filename))
     sys.path.insert(0, path)
     try:
-        loader = importlib.machinery.SourceFileLoader(modname, filename)
-        module = loader.load_module()
+        previous_modules = copy(sys.modules)
+        try:
+            loader = importlib.machinery.SourceFileLoader(modname, filename)
+            module = loader.load_module()
+        finally:
+            sys.modules = previous_modules
     finally:
         sys.path.remove(path)