diff --git a/onnxscript/testing/__init__.py b/onnxscript/testing/__init__.py
index e62a44d9a..bacfe9777 100644
--- a/onnxscript/testing/__init__.py
+++ b/onnxscript/testing/__init__.py
@@ -8,6 +8,7 @@
 ]
 
 import difflib
+import math
 from typing import Any, Collection, Sequence
 
 import google.protobuf.message
@@ -448,6 +449,14 @@ def assert_onnx_proto_equal(
                         error_message = f"Field {field} index {i} in sequence not equal. type(a_value_i): {type(a_value_i)}, type(b_value_i): {type(b_value_i)}, a_value_i: {a_value_i}, b_value_i: {b_value_i}"
                         raise AssertionError(error_message) from e
                 elif a_value_i != b_value_i:
+                    if (
+                        isinstance(a_value_i, float)
+                        and isinstance(b_value_i, float)
+                        and math.isnan(a_value_i)
+                        and math.isnan(b_value_i)
+                    ):
+                        # Consider NaNs equal
+                        continue
                     error_message = f"Field {field} index {i} in sequence not equal. type(a_value_i): {type(a_value_i)}, type(b_value_i): {type(b_value_i)}"
                     for line in difflib.ndiff(
                         str(a_value_i).splitlines(), str(b_value_i).splitlines()
@@ -459,5 +468,13 @@ def assert_onnx_proto_equal(
         ):
             assert_onnx_proto_equal(a_value, b_value)
         elif a_value != b_value:
+            if (
+                isinstance(a_value, float)
+                and isinstance(b_value, float)
+                and math.isnan(a_value)
+                and math.isnan(b_value)
+            ):
+                # Consider NaNs equal
+                continue
             error_message = f"Field {field} not equal. field_a: {a_value}, field_b: {b_value}"
             raise AssertionError(error_message)