Pilonidal sinus is a well recognised chronic inflammatory condition which commonly affects the natal cleft and finger web space. Pilonidal sinus of the penis is a rare clinical entity; few cases have been reported previously. The treatment strategy is almost the same as treating any pilonidal sinus and involves total excision of the sinus. Our diagnosis was established on the histopathological findings rather than a clinical-based diagnosis, Follow-up is advisable since the recurrence rate is high. Our case report is one of few cases reported on pilonidal sinus all over the world. Our patient had total excision of the sinus with complete recovery.