We present a case of congenital of flexor pollicis longus agenesis without thenar hypoplasia in a 12-year-old girl with no history of trauma. Two-staged corrective surgery was planned. In the first stage, the flexor pulley was reconstructed using silicone followed by the second stage 3 months later when flexor pollicis longus reconstruction was performed using tendon transfer of the flexor digitorum superficialis. The patient completed post-operative physiotherapy and the result of the surgical treatment in both functional and cosmetic aspects was, in the authors’ opinion, excellent.