We present a 62-year-old female patient who had an anatomic variation in the median nerve of the left hand. During surgery for releasing the left carpal tunnel, an abnormally high level of origin of the thenar muscular branch of the median nerve was detected, at 2.5 cm above the proximal border of transverse carpal ligament. It traveled between the medial side of the flexor carpi radialis tendon and median nerve and entered the carpal tunnel. After exiting the carpal tunnel distally, the nerve, was noted to course towards the thenar area. Such variations in the median nerve should be kept in mind while performing carpal tunnel release.