Congenital prepubic sinus is a rare congenital anomaly situated in the midline of the lower abdomen. We report a case of congenital prepubic sinus, closely associated with a urachal remnant. Preoperative magnetic resonance imaging showed clearly that the sinus tracked the urachus caudally. This finding supports the theory that the anomaly is caused by abnormal remnant tissue originating from the cloacal membrane, which tracks the allantois duct caudally along with fetal longitudinal growth.