The Achilles tendon is the strongest and largest tendon in the body. Rupture of this tendon usually occurs in the third and fourth decade and can be significantly debilitating. Repair of neglected ruptures of Achilles tendon pose a challenge to the orthopaedic surgeon due to the retraction and atrophy of the ends of the tendon. Various surgical procedures have been described which include VY plasty, fascia lata, peroneus brevis, plantaris tendon, flexor digitorum longus, flexor hallucis longus, allograft, and synthetic materials. We carried out a prospective study to compare the results of peroneus brevis transfer with flexor hallucis longus transfer in the management of neglected ruptures of Achilles tendon. Forty-seven patients who had neglected ruptures of Achilles tendon were included in this study. They were randomly divided into two groups; the first group underwent peroneus brevis transfer (24 patients) and the second group had flexor hallucis longus transfer (23 patients). Patients were assessed using the Quigley's scoring system. We conclude that Flexor hallucis longus transfer is better than peroneus brevis transfer as it is a long, durable tendon which is much stronger when compared to other tendon transfers. Flexor hallucis longus acts in the same axis as the Achilles tendon, is in the same gait phase and is in close proximity, making harvesting of the tendon easy.