Equine septic fungal arthritis is poorly documented in the literature. There is absence of efficacy and safety data for anti-fungal medications, highlighting the importance of documenting this case. A 15-year-old Irish sport horse gelding presented moderately lame at the walk on the left hindlimb 13 days after intra-articular medication of the left tarso-crural joint with triamcinolone and hyaluronic acid. Radiography revealed an osteochondral fragment at the distal intermediate ridge of the tibia and shallow subchondral bone defect on the medial trochlear ridge. Synoviocentesis yielded a turbid sample with an elevated total nucleated cell count (49x109cells/L; total neutrophil count of 62.8%). Arthroscopic lavage of the tarsocrural joint (TCJ) was performed. Ceftriaxone was administered and systemic antimicrobials initiated. The fungus Wickerhamomyces anomalus was identified on culture. The horse was subsequently intensively treated with antimicrobial and anti-fungal medications, both systemically and intra-articularly over the following 60 plus days. Multiple subsequent synovial cultures revealed the persistence of the fungal organism, until a negative culture on day 55. However, on day 113, a non-weight bearing lameness at trot was present, and a further positive synovial fungal culture. Radiographs revealed a lytic lesion at the distal tibia with marked progression. The horse was euthanised on day 126.