We aimed to report surgical outcomes and analyze prognostic factors of medial toe excision for polysyndactyly of the fifth toe. We reviewed the details of 139 consecutive patients who underwent surgery for postaxial polydactyly of the foot from 2009 to 2018. Among these, 83 patients (90 feet) with polysyndactyly of the fifth toe, treated by medial toe excision (between the duplicated toes) and reconstruction of the fourth web space using a dorsal rectangular flap, were included. The toe alignment and stability were restored by chondroplasty and soft tissue balancing without an osteotomy. A full-thickness skin graft was performed in 52 feet. The mean age at surgery was 27.1 ± 17.5 months and the mean duration of follow-up was 42.8 ± 24.9 months. At the last follow-up, a relatively small size of the reconstructed toe was observed in 19 feet (19/90, 21.1%). Proximal duplication level (metatarsal or proximal phalanx type) and preoperative hypoplasia of the remaining toe were related to the small postoperative size. Valgus deformity of the remaining toe was observed in 2 feet (2/90, 2.2%). We observed 17 cases with delayed healing or early postoperative wound infection. Among these, 7 cases (7/90, 7.8%) showed postoperative thickening or advancement of the web, which was not observed in cases without wound problems. No cases had functional disturbance or pain. The overall surgical outcomes were satisfactory without an osteotomy. Patients with a proximal duplication level or preoperative hypoplasia of the remaining toe should be informed of its possible small size postoperatively. Level IV, retrospective case series.