Median raphe cyst is an uncommon developmental anomaly that can develop anywhere along the midline of the external genitals. Only a few hundred cases have been published in the English literature and the lack of awareness of this entity can lead to confusion and misdiagnosis. We report here a case of median raphe cyst located in the midline of the anterior scrotum of a 35-year-old man. Clinically, the patient presented with a scrotal mass increasing substantially in size over two days associated with tenderness, skin erythema, and scrotal pain. Radiologic interpretation of a sonogram and computed tomography scan suggested a thrombosed vessel. The patient was diagnosed with septic thrombophlebitis associated with overlying cellulitis. Despite conservative therapy with antibiotics, the patient developed pyrexia, tachycardia, and leukocytosis prompting surgical excision of the lesion. Histopathologic examination revealed an infected median raphe cyst. The cyst wall was lined by a stratified epithelium that included numerous Alcian blue positive goblet cells. The epithelial cells showed reactive changes with infiltration by numerous neutrophils. Our objective is to bring attention to and thereby facilitate the diagnosis of this unusual entity.