Background: Popliteal pterygium syndrome (PPS) is a rare congenital disorder characterized by orofacial, cutaneous, musculoskeletal, and genital anomalies. Surgical interventions are necessary to address the severe knee flexion contracture and equinovarus deformity, but there are no established treatment guidelines. Methods: We present the case of a one-year-old patient with PPS and discuss the challenges in managing the knee deformity. The surgical option chosen for the unilateral knee contracture of 80° consisted of skin management by a large Z-plasty, lengthening of popliteal vessels by grafts, lengthening of the tibial and peroneal nerves by autografts and allografts, capsular releases, and tendon releases to improve mobility and preserve foot sensibility. Results: With a three-year follow-up, the surgical interventions resulted in proper ability to walk freely. Wearing of a foot orthesis was necessary to balance the leg length differences and support the midfoot deformity. Furthermore, sensation of the foot could be restored in terms of touch sensibility and perfusion was always stable during growth. Discussion: The treatment of PPS requires a multidisciplinary approach, considering the rarity and complexity of the syndrome. Surgical interventions aim to release contractures, correct deformities, and preserve foot sensibility. Each treatment option has its advantages and disadvantages, highlighting the need for individualized care.