Here, we report a case of pyoderma gangrenosum of the penis which was difficult to distinguish from Fournier gangrene. The patient was a 54-year-old male who was aware of redness and swelling of the glanspenis for 1 month prior to a consultation at our department. Although he was diagnosed with herpes and treated at a nearby hospital, his symptoms did not improve. Subsequently, the patient visited our department following the onset of pain and fever. During his initial consultation, he had a fever of 39 °C as well as redness and swelling of the glans penis with partial spontaneous purulent discharge. His blood test revealed an elevated white blood cell count (20, 000/μl) and C-reactive protein (19.1 mg/dl). Because Fournier gangrene was suspected, administration of broad-spectrum antimicrobial agents was initiated but proved to be ineffective. An abscess (2 cm in diameter) was also noted in the umbilical region.Enterococcus faecalis was detected by the bacterial culture ; and therefore, Fournier gangrene was diagnosed. A partial penectomy was performed to control the infection. Pathological findings showed only non-specific inflammation ; however, fever persisted postoperatively and blood test results showed no improvement. Furthermore, new abscess lesions emerged on the right heel and back. Because the re-performed abscess bacterial culture test result was negative, pyoderma gangrenosum was suspected, and he was started on oral prednisolone (20 mg/day). On the following day, his fever subsided and his blood test results also showed improvement. A final diagnosis of pyoderma gangrenosum was ultimately made.