Vaginal agenesis is known as one of the Müllerian anomalies. Müllerian anomalies occur during gonadal development and differentiation, and may lead to complex outcomes. McKusick-Kaufman syndrome (MKS) is an autosomal recessive multiple malformation syndrome characterized by Müllerian anomalies with hydrometrocolpos (HMC) and postaxial polydactyly (PAP). We report a case of a female newborn that developed hydronephrosis and respiratory distress due to compression of the cystic mass and underwent surgery on postpartum day 3. Pull-through vaginoplasty was performed with an abdomino-perineal approach. We report the unique treatment approach in this case.