Lymphatic malformation/lymphangioma of the scrotum is rare. It is caused by lymphatic abnormalities and the most common sites are the neck and axilla. The scrotum is one of the most uncommon sites. We report the case of a 12-year-old boy with pathologically confirmed cystic lymphangioma/lymphatic malformation in the scrotum. The diagnosis was suspected from ultrasonography and magnetic resonance imaging. The most common cause of a cystic mass in the scrotum is scrotal hydrocele, but cystic lymphangioma/lymphatic malformation should be considered as a differential diagnosis for multicystic scrotal mass.