Congenital prepubic sinus is a very rare urogenital anomaly that manifests as a tubular structure of varying histological findings that drains to the skin overlying the pubic symphysis. This tract has been observed to course above, below or, in only a handful of cases, directly through the pubis. We report a case of congenital prepubic sinus with this unusual transpubic course in an 18-year-old man. The patient was initially taken to the operating room for excision of a presumed inclusion cyst. At the time of surgery, the collection was found to track proximally and was excised down to the level of the pubic symphysis. Subsequent magnetic resonance (MR) imaging established the diagnosis of congenital prepubic sinus. We describe the different anatomical courses of congenital prepubic sinus, hypotheses of its pathogenesis, and the use of MR imaging in both diagnosis and surgical planning.