Rationale: Neonatal cholestasis is one of the most serious diseases in infancy. Progressive familial intrahepatic cholestasis (PFIC) is a disease that leads to intrahepatic cholestasis. It is one of the common causes of neonatal cholestasis in addition to biliary atresia (BA). The differential diagnosis of neonatal cholestasis is clinically challenging for pediatricians. Patient concerns: A 4-month-old female presented with severe jaundice, pruritus, and pale stool for 20 days. Abnormally strong echoes near the portal area, an abnormally small gallbladder with an irregularly stiff wall, and splenomegaly were identified on abdominal ultrasound. Blood tests showed elevated alanine aminotransferase, total bilirubin, conjugated bilirubin, gamma-glutamyltranspeptidase, and total bile acid levels. Diagnosis: Intraoperative cholangiography showed BA. ABCB4 gene mutation IVS13+6G>A/G was confirmed by genetic testing. The patient was diagnosed with BA combined with PFIC3. Interventions: Kasai portoenterostomy and ursodeoxycholic acid were used for treatment. Outcomes: Her clinical symptoms and blood tests improved gradually. No recurrence was noted during 1 year of follow-up. Lessons: Additional examinations, such as genetic testing, should be considered in patients with BA who had refractory jaundice after Kasai portoenterostomy in order to exclude intrahepatic cholestasis.