This report describes fibrous cyst lining injection and extracorporeal shock wave therapy (ESWT) of a medial femoral condyle (MFC) subchondral cystic lesion (SCL) resulting in catastrophic MFC fracture in an Arabian mare. The mare was presented for evaluation of a severe hind limb lameness of approximately 4 months duration. On presentation, a non-weight bearing lameness of the left hind limb with severe effusion and soft tissue swelling of the stifle region was noted. Radiographic evaluation of the stifle revealed a large SCL of the MFC with associated osteoarthritis. Arthroscopic guided intra-lesional injection of the SCL with corticosteroids and autologous bone marrow concentrate was performed followed by ESWT of the MFC. The mare was discharged walking comfortably 48-hours post-operatively. An acute increase in lameness was noted 14 days post-operatively. Imaging revealed catastrophic fracture of the left MFC. Possible mechanisms leading to failure of the MFC secondary to the described treatment are discussed.