Pyoderma gangrenosum (PG) shows characteristic non-infectious ulcers that are commonly associated with systemic diseases such as inflammatory bowel diseases, myeloproliferative disorders or aortitis syndrome. The typical clinical appearance is undermining ulcers with reddish and irregular borders on the legs. As PG has these notable signs, the diagnosis is relatively easy and its treatment depends on the severity of underlying complications. We report a case of a 60-year-old Japanese man, diagnosed with bullous PG, who also had been suffering from myeloperoxidase antineutrophil cytoplasmic antibody-positive microscopic polyangiitis and pulmonary aspergillosis. This case displayed soft whitish ulcers that existed on the rough ulcer base, with irregular borders, on his bilateral dorsal hands. Initially, it seemed to be cutaneous secondary aspergillosis because the host was already infected with pulmonary aspergillosis in both lungs. The differential diagnosis of PG from aspergillosis was from the sterile bullae or neutrophilic bullae on his right forearm, which evolved into ulcers in a few days. This case was finally diagnosed as bullous PG and a topical glucocorticoid was very effective to epithelize the ulcers in 2–3 weeks.