BackgroundPigmented villonodular synovitis is a rare yet locally invasive disorder impacting synovial tissues. This case report delineates the atypical manifestation of pigmented villonodular synovitis in the talonavicular joint, detailing its diagnostic complexity and successful management.Case presentationA 56-year-old Iranian patient with a 4-year history of chronic ankle pain, initially diagnosed with degenerative joint disease post-trauma based on imaging, underwent talonavicular fusion surgery. An unexpected pigmented villonodular synovitis mass was encountered during the procedure. Subsequent interventions encompassed tumor resection, talonavicular joint fusion, and allograft bone grafting. Despite the initial intervention, persistent pain and nonunion necessitated a secondary procedure, involving joint surface curettage and autograft bone grafting. At the 12-month follow-up, the patient remained pain-free without tumor recurrence.ConclusionThis case report highlights the significance of considering pigmented villonodular synovitis as a crucial differential diagnosis in chronic ankle pain, even when there is evidence of degenerative joint disease and a history of trauma. Magnetic resonance imaging serves a crucial role in accurate diagnosis. Treatment necessitates precise tumor removal, appropriate bone grafting techniques and secure fixation.Level of evidence: IV.