Median raphe cysts of the perineum are rare congenital anomalies of the male genitalia, which form during embryological development, and can be found in the midline from the distal penis to the perineum. However, the incidence of median raphe cyst is likely under-reported and under-recognized. We report on the case of a median raphe cyst extending from the scrotum to the perineum with recurrent infection and purulent discharge in a 28-year-old man, which first developed at the age of 5 years. We believe it is important that urologists recognize median raphe cysts and have knowledge of their management in order to provide appropriate information to patients.