We report an intra-articular ganglion cyst (IAGC) presenting as knee pain and a mass in a patient with longstanding Juvenile Idiopathic Arthritis (JIA). We could not find a similar case of an IAGC occurring in the knee of JIA patients in the literature. IAGC may need to be included as a possibility in patients with inflammatory arthritis with new-onset knee pain, especially in those with a palpable mass. MRI was useful in distinguishing IAGC from more worrisome causes of a knee mass. Orthopedic input was helpful in diagnosis and treatment. In addition, methotrexate therapy was effective in bringing about a long-lasting remission.