Median raphe cyst is a rare, benign congenital cyst presenting most commonly on the ventral aspect of penile shaft. These lesions present mostly in young men, whereas some cases in children have also been reported. The occurrence of a ventral cystic lesion of the penis should alert the clinician to the diagnosis of a median raphe cyst. The lesions, which are most common near the glans penis, may occur anywhere from the urethral meatus to the anus. Surgical excision is the treatment of choice. We here by report the case of a nine year old boy with median raphe cyst of penis. Median raphe cysts are rarely reported since they are usually asymptomatic.