Popliteal pterygium syndrome is a rare congenital disorder that consists of popliteal webs and craniofacial, genitourinary and extremity anomalies. Only moderate successful surgical excision of the fibrotic band within the popliteal web has been reported because the nerves and vessels in the affected site are short and displaced into the web and they are attached to adjacent tissues. We performed hamstring tenotomy on the ischial tuberosity, tenotomy of the flexor hallucis longus and Z-lengthening of the Achilles tendon on the ankle in our patient, and this was followed by gradual correction using an Ilizarov external fixator. Full extension of the knee joint was achieved at the ninth postoperative week. However, some recurrence of flexion contracture was noted at two years follow-up. Gradual soft tissue lengthening with an Ilizarov external fixator can be one of the optimal procedures when excision of a fibrous band and Z-plasty are not possible due to severe adhesion of the nerves and vessels into a fibrotic band. However, a cautious approach is recommended when considering the high risk of recurrence.