We present a case of intra- and extra-articular localized pigmented villonodular synovitis (PVNS) of the right knee joint separately. A 14-year-old girl presented with a painful mass over the medial aspect of the right knee. MRI demonstrated nodular masses located in the anteromedial area of the knee joint and on the surface of the deep medial collateral ligament outside the joint. Arthroscopic and open synovectomy were performed for both lesions. Histopathology confirmed diagnosis of localized PVNS and pigmented villonodular bursitis, respectively. Our case highlights that localized PVNS are likely to occur in intra- and extra-articular regions separately.