diff --git a/tools/migration/ctoolchain_comparator_lib.py b/tools/migration/ctoolchain_comparator_lib.py
index 0adefd3a..eb47305e 100644
--- a/tools/migration/ctoolchain_comparator_lib.py
+++ b/tools/migration/ctoolchain_comparator_lib.py
@@ -52,6 +52,11 @@ def _check_with_feature_set_equivalence(before, after):
 
 
 def _check_tool_equivalence(before, after):
+  """Compares two "CToolchain.Tool"s."""
+  if before.tool_path == "NOT_USED":
+    before.tool_path = ""
+  if after.tool_path == "NOT_USED":
+    after.tool_path = ""
   if before.tool_path != after.tool_path:
     return False
   if set(before.execution_requirement) != set(after.execution_requirement):
@@ -297,9 +302,11 @@ def _compare_tool_paths(tool_paths_before, tool_paths_after):
   tool_to_path_before = {}
   tool_to_path_after = {}
   for tool_path in tool_paths_before:
-    tool_to_path_before[tool_path.name] = tool_path.path
+    tool_to_path_before[tool_path.name] = (
+        tool_path.path if tool_path.path != "NOT_USED" else "")
   for tool_path in tool_paths_after:
-    tool_to_path_after[tool_path.name] = tool_path.path
+    tool_to_path_after[tool_path.name] = (
+        tool_path.path if tool_path.path != "NOT_USED" else "")
 
   tool_names_before = set(tool_to_path_before.keys())
   tool_names_after = set(tool_to_path_after.keys())
diff --git a/tools/migration/ctoolchain_comparator_lib_test.py b/tools/migration/ctoolchain_comparator_lib_test.py
index 06645b0a..c81ff478 100644
--- a/tools/migration/ctoolchain_comparator_lib_test.py
+++ b/tools/migration/ctoolchain_comparator_lib_test.py
@@ -1665,6 +1665,45 @@ def test_action_config_implies_preserves_order(self):
       self.assertIn("* Action config 'config' differs before and after",
                     mock_stdout.getvalue())
 
+  def test_unused_tool_path(self):
+    first = make_toolchain("""
+        tool_path {
+          name: "empty"
+          path: ""
+        }
+    """)
+    second = make_toolchain("""
+        tool_path {
+          name: "empty"
+          path: "NOT_USED"
+        }
+    """)
+    mock_stdout = StringIO()
+    with mock.patch("sys.stdout", mock_stdout):
+      compare_ctoolchains(first, second)
+      self.assertIn("No difference", mock_stdout.getvalue())
+
+  def test_unused_tool_path_in_tool(self):
+    first = make_toolchain("""
+        action_config {
+          config_name: 'config'
+          tool {
+            tool_path: ''
+          }
+        }
+    """)
+    second = make_toolchain("""
+        action_config {
+          config_name: 'config'
+          tool {
+            tool_path: 'NOT_USED'
+          }
+        }
+    """)
+    mock_stdout = StringIO()
+    with mock.patch("sys.stdout", mock_stdout):
+      compare_ctoolchains(first, second)
+      self.assertIn("No difference", mock_stdout.getvalue())
 
 if __name__ == "__main__":
   unittest.main()