Background: Renal agenesis is a congenital malformation that occurs due to the inhibition of metanephric blastema induction due to a decrease in ureteric bud activity. Although renal agenesis is not very rare, unilateral renal agenesis with ureterocele occurs rarely, and the coexistance of unilateral renal agenesis, ureterocele, and blind ended proximal ureter is very rare. Recently, we experienced a case of left renal agenesis with huge ureterocele, blind ended proximal ureter, and duplicated ureter on Computed tomography (CT) of a 17-year-old man who visited our emergency department with hematuria. Ureterocelectomy and nephrectomy were performed, and a translocation of seminal vesicle was also observed. This case is a very rare case, so we judged that it may be helpful in making treatment decisions in similar cases later. Case summary: A 17-year-old man without specific medical history visited our emergency department with hematuria and voiding difficulty. CT showed left ectopic kidney, megaureter and the blind ended proximal ureter. After ureterocelectomy and nephrectomy, pathological examination revealed seminal vesicles in the periphery of the kidney. After one year, the patient has no complications and no complaining symptoms complaints without any abnormal finding of follow up imaging test. Conclusions: This case report focuses on the treatment of renal agenesis with ureterocele, blind ended proximal ureter, duplicated megaureter and translocation of seminal vesicle. This rare case of treatment will be helpful in the determination of treatment for similar cases in the future. To establish standard treatment, data accumulation and well-designed studies are required.