diff --git a/ceci/utils.py b/ceci/utils.py
index e039a40..21a74ea 100644
--- a/ceci/utils.py
+++ b/ceci/utils.py
@@ -3,23 +3,36 @@
 
 @contextmanager
 def extra_paths(paths, start=True):
+    # allow passing a single path or
+    # a list of them
     if isinstance(paths, str):
         paths = paths.split()
 
+    # On enter, add paths to sys.path,
+    # either the start or the end depending
+    # on the start argument
     for path in paths:
         if start:
             sys.path.insert(0, path)
         else:
             sys.path.append(path)
 
+    # Return control to caller
     try:
         yield
+    # On exit, remove the paths
     finally:
         for path in paths:
-            if start:
-                sys.path.remove(path)
-            else:
-                remove_last(sys.path, path)
+            try:
+                if start:
+                    sys.path.remove(path)
+                else:
+                    remove_last(sys.path, path)
+            # If e.g. user has already done this
+            # manually for some reason then just
+            # skip
+            except ValueError:
+                pass
 
 def remove_last(lst, item):
     """
diff --git a/tests/test_python_paths.py b/tests/test_python_paths.py
index 0ca2e8f..d8f4a93 100644
--- a/tests/test_python_paths.py
+++ b/tests/test_python_paths.py
@@ -67,7 +67,8 @@ def test_extra_paths():
         assert sys.path[0] == p[1]
         assert sys.path[1] == p[0]
 
-    assert p not in sys.path
+    for p1 in p:
+        assert p1 not in sys.path
     assert sys.path == orig_path
 
     try:
@@ -78,7 +79,8 @@ def test_extra_paths():
     except MyError:
         pass
 
-    assert p not in sys.path
+    for p1 in p:
+        assert p1 not in sys.path
     assert sys.path == orig_path
 
 
@@ -89,7 +91,8 @@ def test_extra_paths():
         assert sys.path[-1] == p[1]
         assert sys.path[-2] == p[0]
 
-    assert p not in sys.path
+    for p1 in p:
+        assert p1 not in sys.path
     assert sys.path == orig_path
 
     try:
@@ -103,4 +106,22 @@ def test_extra_paths():
     assert p not in sys.path
     assert sys.path == orig_path
 
+    # check that if the user removes the path
+    # themselves then it is okay
+    p = ['xxx111yyy222', 'aaa222333']
+    with extra_paths(p, start=True):
+        sys.path.remove('xxx111yyy222')
+
+    assert sys.path == orig_path
 
+    # check only one copy is removed
+    sys.path.append("aaa")
+    tmp_paths = sys.path[:]
+    p = "aaa"
+    with extra_paths(p, start=True):
+        pass
+
+    assert sys.path == tmp_paths
+
+    with extra_paths(p, start=False):
+        pass