Background: Zinner's syndrome represents a rare developmental anomaly of the urogenital tract, characterized by the triad of unilateral renal agenesis, ipsilateral seminal vesicle cyst, and ipsilateral ejaculatory duct obstruction. This syndrome arises from malformations of the mesonephric duct during embryogenesis. Magnetic resonance imaging (MRI) plays a pivotal role in confirming the diagnosis by revealing the presence of seminal vesicle cysts and identifying ejaculatory duct obstructions, while computed tomography (CT) scans confirm renal agenesis. Case description: Here, we report a case of a 22-year-old gentleman who reported to our department with complaints similar to prostatitis but was eventually diagnosed with Zinner's syndrome, which was managed with antibiotics, and prompt symptomatic relief was achieved by the patient. Conclusion: This case report highlights the importance of accurate diagnosis and management of this condition. While conservative management is common, some cases necessitate minimally invasive surgery for optimal treatment.