Hansenula anomala (H. anomaly) is part of the normal flora in the alimentary tract and throat. It has been reported to be an organism causing opportunistic infections in immunocompromised patients. However, cases of fungal arthritis caused by H. anomala are rare. We encountered a case of H. anomala arthritis in a 70-year-old man who was treated with an empirical antibiotic treatment and surgery under the impression of septic arthritis. However, the patient did not improve after antibiotic therapy and surgery. Consequently, knee joint aspiration was performed again, which identified fungal arthritis caused by H. anomala. It was treated successfully with amphotericin B and fluconazole. When treating arthritis patients with diabetes, it is important to consider the possibility of septic arthritis by H. anomala and provide the appropriate treatment.