Pigmented villonodular synovitis (PVNS) is a benign but rare proliferative disorder of the synovium. It commonly occurs in the adult population and usually presents as a monoarticular disease. There are two types of PVNS, namely the localised and diffused type. The disease is often misdiagnosed due to its rarity especially in paediatric patients. Knee involvement in PVNS is the commonest form in children although other joints such as hip, foot, ankle, hip, sacroiliac joint and concurrent multiple joint involvements have also been reported. PVNS in paediatric patients is often misdiagnosed as septic arthritis, juvenile rheumatoid arthritis and bone sarcoma, and the diagnosis is usually often made late due to its vague presentation. The majority of PVNS cases are managed by surgery either via open or arthroscopic synovectomy except in a few paediatric patients as described in the literature. This case report of PVNS is of a knee in 11- year-old boy who was initially treated as septic arthritis. The synovium appearance mimicked the features of PVNS during a knee arthrotomy washout, and histopathological examination confirmed the diagnosis. The knee symptoms had significantly improved without additional surgery, and good functional knee motion was achieved, with no sign of recurrence, after two years of follow-up.