BACKGROUND Pigmented villonodular synovitis (PVNS) is an uncommon disease that usually occurs in large joints, and involvement of the subtalar joint is rare. The lack of comprehensive knowledge of subtalar joint PVNS could lead to misdiagnosis. METHODS We present a 64-year-old woman who, at her first visit, complained of discomfort in the right ankle when she walked. Based on the physical signs and X-ray report, the physician failed to make the suspected diagnosis of PVNS. Eighteen months later, the patient returned with a complaint of a mass in her right lateral malleolus with intermittent blunt pain. The X-ray presented an osteophyte formation and soft tissue calcification at the margin of the subtalar joint. The laboratory tests were normal, whereas magnetic resonance imaging (MRI) showed a low-intensity area on both T1- and T2-weighted images. A suspected diagnosis of PVNS was made and later confirmed by postoperative pathology. Subsequently, the patient received radiotherapy with 32 Gy in 16 fractions. At 6 mo postoperatively, the patient only complained of discomfort after walking three blocks. The American Orthopedic Foot and Ankle Society Ankle-Hindfoot score was 97. CONCLUSIONS MRI is necessary for the diagnosis of PVNS. Early soft tissue calcification and painless joint swelling should be of concern.