Background: Biliary atresia (BA) is a condition that obstructs biliary flow. If it is not corrected surgically, it can cause cirrhosis and death before 2 years of age. In Mexico, since 2013, the stool color card (SCC) was incorporated into the National Health Card (NHC) for the screening of BA. This study aimed to evaluate the impact of SCC for the detection of BA before and after its incorporation to the NHC. Methods: This is an ambispective, analytical observational study. We included patients with BA treated in two pediatric specialized hospitals. We compared the age of reference, diagnosis, and surgery before and after incorporation of the SCC. Furthermore, a questionnaire was made for the parents to know their perception about the SCC. Results: In 59 children, there was no difference among the time of diagnosis (75 vs. 70 days of life) or at the time of the surgery (84 vs. 90 days of life) between the pre-and post-implementation of the SCC on the NHC. The questionnaire showed that 10 (30%) of the parents received information about the use of the SCC and only 13 (38%) identified the abnormal stool. Conclusions: This study did not show changes in time for the timely detection of BA using SCC. Therefore, it is necessary to reinforce the program in the three levels of care in our country.