Pyoderma gangrenosum is a rare, destructive, inflammatory disorder, which presents with progressively enlarging ulcers, single or multiple, mostly involving the lower extremities. It may occur alone or in association with other system diseases like inflammatory bowel disease, polyarthritis, gammopathy, etc. A case of pyoderma gangrenosum in a young male presenting with a single ulcer on the glans penis, an unusual site, without any systemic association is being reported. The prolonged history, typical raised, tender, undetermined border along with histopathological confirmation helped in clinching the diagnosis. The unusual site made it imperative to differentiate it from the common sexually transmitted ulcerative disorders and also from lupus vulgaris and squamous cell carcinoma of the penis. The ulcer showed improvement with a combination of systemic steroid and dapsone.