BackgroundTo date, the optimal operative treatment for mucous cysts of the lesser toes (MCLT) has not been discussed in detail, although many previous studies have focused on treating finger lesions. Therefore, we evaluated the operative outcomes of two different procedures for MCLT: cyst excision with osteophytectomy and cyst excision with distal interphalangeal (DIP) fusion. MethodsWe retrospectively reviewed and compared the clinico-radiographic outcomes of patients who underwent cyst excision with osteophytectomy (group 1, 22 cases) or cyst excision with DIP fusion (group 2, 16 cases) for MCLT between January 2010 and August 2021. The minimum follow-up duration for inclusion in the study was 12 months. Clinical outcomes were evaluated using the American Orthopedic Foot and Ankle Society (AOFAS) lesser toes metatarsophalangeal-interphalangeal scale and the Foot and Ankle Ability Measure (FAAM) Activities of Daily Living (ADL) subscale. We also collected information on postoperative recurrence and operation-related complications. ResultsThe preoperative and postoperative AOFAS and FAAM-ADL scores were not significantly different between the two groups (P > 0.05, each). However, the postoperative recurrence rate was 31.8 % in group 1 (7 of 22 cases), whereas no recurrence was observed in group 2. Every recurrence occurred within 8 postoperative weeks (mean, 4.8 weeks; range, 3–8 weeks). Nonunion of the fusion site was observed in one patient (6.3 %). ConclusionWe confirmed that postoperative recurrence was significantly lower in the case of cyst excision with DIP fusion than in cyst excision with osteophytectomy for the treatment of MCLT. Clinical outcomes were not significantly different between the two procedures. Level of evidenceLevel III, retrospective comparative study.