Background: Seminal vesicle cyst is an extremely rare condition, which is frequently congenital and associated with Zinner's syndrome. This syndrome represents a constellation of seminal vesicle cyst, ipsilateral or contralateral renal agenesis or renal dysplasia, ureteral ectopia, and ejaculatory duct obstruction. We report a young symptomatic patient undergoing robot-assisted laparoscopic excision of a huge seminal vesicle cyst during which an atrophic ipsilateral kidney was discovered incidentally and managed by nephroureterectomy in the same session without changing trocar positions. Case Presentation: A 23-year-old male patient presented with a 2-year history of lower urinary tract symptoms, perineal pain, and recurrent urinary tract infections. Ultrasonography revealed the absence of left kidney and a fluid-filled cystic lesion located behind the bladder on the left side, which was consistent with cystic dilatation of the left seminal vesicle. MRI confirmed the diagnosis of a huge cystic structure originating from the left seminal vesicle and identified the presence of a rudimentary left ureter without an associated renal unit. Cystoscopy revealed bulging of the bladder neck at 6 o'clock position and the ureteral orifices at normal positions and configurations. Based on these findings, the clinical diagnosis was established as Zinner's syndrome. The present case was performed by Da Vinci Si robotic platform using the 5-trocar technique. Conclusion: Robot-assisted laparoscopic excision is a safe and feasible option to treat large seminal vesicle cysts, which may be a component of Zinner's syndrome. Simultaneous upper urinary tract interventions, such as nephroureterectomy, can be employed by redocking the robot and repositioning the patient, using the same layout of robotic trocars.