Crossed fused renal ectopia and the presence of a supernumerary kidney are both rare congenital variants that are often asymptomatic but may be associated with other developmental anomalies. Here we present a case of a 20-year-old male with a known diagnosis of crossed fused renal ectopia as well as a history of imperforate anus and tethered spinal cord treated in infancy. He presented to the emergency room with symptoms of flank pain, and a noncontrast computed tomography (CT) scan revealed a 4-mm stone in the distal left ureter. CT scan also revealed that the patient's right kidney was not crossed and fused to the left kidney as previously believed, but rather it was crossed and fused to a supernumerary kidney abutting the inferomedial aspect of an orthotopic left kidney. This is a unique example of two rare coexisting renal anomalies not previously detected on a nuclear medicine renal scan and serial renal ultrasounds obtained earlier in the the patient's life.