Median raphe cyst (MRC) of the perineum is rare congenital midline cyst of the male genitalia. MRC is thought to be caused by congenital alterations in the embryologic development of the male genitalia during fetal life. MRC can be found on the midline position between the urethral meatus and the anus. The lesion can be cystic, but sometimes it looks like an elongated configuration called a raphe canal. Diagnosis in childhood is particularly rare because they are usually asymptomatic, but some cases have reportedly been identified after infection. Although conservative treatment can be possible in small asymptomatic lesions, the treatment of choice is simple excision followed by primary closure in symptomatic cases. We describe here the case of 2-year-old boy presented at our institution with a 10-month history of anomaly of the perineal median raphe, which was treated by surgical excision.