Background The goal of this study was to investigate the anatomy of the peroneal artery and its perforators, and to report the clinical results of reconstruction with peroneal artery perforator flaps. Methods The authors dissected 4 cadaver legs and investigated the distribution, course, origin, number, type, and length of the perforators. Peroneal artery perforator flap surgery was performed on 29 patients. Results We identified 19 perforators in 4 legs. The mean number of perforators was 4.8 per leg, and the mean length was 4.8 cm. Five perforators were found proximally, 9 medially, and 5 distally. We found 12 true septocutaneous perforators and 7 musculocutaneous perforators. Four emerged from the posterior tibia artery, and 15 were from the peroneal artery. The peroneal artery perforator flap was used in 29 patients. Retrograde island peroneal flaps were used in 8 cases, anterograde island peroneal flaps in 5 cases, and free peroneal flaps in 16 cases. The mean age was 59.9 years, and the defect size ranged from 2.0 cm×4.5 cm to 8.0 cm×8.0 cm. All the flaps survived. Five flaps developed partial skin necrosis. In 2 cases, a split-thickness skin graft was performed, and the other 3 cases were treated without any additional procedures. Conclusions The peroneal artery perforator flap is a good alternative for the reconstruction of soft tissue defects, with a constant and reliable vascular pedicle, thin and pliable skin, and the possibility of creating a composite tissue flap.