A 20-month-old Warmblood filly was evaluated for acute onset of a nonweightbearing lameness and swelling of the left hindlimb. Clinical and lameness evaluation and diagnostic intrasynovial anaesthesia isolated the lameness to the left hind metatarsophalangeal region. Radiography and ultrasonography revealed a subchondral cystic lesion of the apical portion of the lateral proximal sesamoid bone associated with oedema and synovial effusion of the metatarsophalangeal joint. Arthroscopic surgical debridement of the subchondral cystic lesion resulted in immediate post operative improvement in the lameness score. Rest and controlled exercise achieved complete resolution of the lameness with the filly being able to start training without apparent lameness. Subchondral cystic lesions of the proximal sesamoid bones can be a cause of nonweightbearing lameness. Surgical debridement resulted in complete resolution of the lameness with a favourable outcome in this case.