Treatment of recurrent carpal tunnel syndrome (CTS) is challenging, especially in a case with recurrent CTS and a neuroma formation. Resection of the neuroma causing the syndrome, reconstruction of the nerve gap of the median nerve, and covering up the reconstructed median nerve with well-vascularized soft tissue for prevention of CTS re-recurrence are the essential procedures. We report a case of recurrent CTS with severe pain due to a neuroma-in-continuity successfully treated using a free anterolateral thigh (ALT) flap with a vascularized lateral femoral cutaneous nerve (LFCN). A 2 cm neuroma existed in the median nerve and was resected. The nerve gap was repaired using a vascularized LFCN included in the ALT flap. The ALT flap was transferred to the wrist to cover the median nerve. The severe pain disappeared completely and the sensory and motor impairment of the median nerve improved 5 months after the free flap surgery, as the Tinel's sign moved distally away from the wrist and disappeared. The result of the Semmes-Weinstein test improved from 5.08 to 4.31 and she was able to flex and extend the right wrist and fingers without pain. CTS did not recur 15 months after the surgery. A free ALT flap with vascularized LFCN allows nerve reconstruction for the median nerve gap created after neuroma resection and coverage of the median nerve with well-vascularized soft tissue to prevent adhesion and CTS recurrence.