Background: While decompressing the median nerve, the thenar motor branch in the transligamentous variation may continue to remain under pressure of the transverse carpal ligament. It is aimed to present the long-term decompression results of patients with transligamentous thenar motor branch. Methods: Between 2020 and 2022, patients diagnosed with severe CTS were included. The thenar motor branch was explored, and in patients with transligamentous variation (n = 16), the thenar motor branch was also decompressed. Grip strength, pinch strength, and the Boston Carpal Tunnel Syndrome Questionnaire were administered pre-surgery, three weeks postoperatively, and at one year. Results: The results showed a significant increase in grip strength and palmar pinch strength and also improved motor functions and quality of life. Conclusions: Despite the release of the transverse carpal ligament in transligamentous type thenar motor branch variations, motor strength may continue to decrease. It is suggested that in these patients, the ligament piece on the motor branch should also be excised additionally. Level of Evidence: Level IV, Risk/Prognostic study.