Seminal vesicle cyst is an extremely rare disease. Its association with ipsilateral renal agenesis is even more exceptional. We present herein one case of a 16-year-old male who presented with a four-month history of lower urinary tract symptoms (LUTSs) and micturition pain. The digital rectal examination revealed a small mass arising from the prostate. The urine culture showed that E. coli is sensitive to all antibiotics tested. Transrectal ultrasound (TRUS) revealed a cystic mass in the outer prostate. Seminal vesicle cyst and left renal agenesis were confirmed by magnetic resonance imaging (MRI). Maximum flow (Q(max)) at uroflow was greater than 15 mL/sec. We therefore decided to manage this disease conservatively with alpha blockers and antibiotics. After 6-month' followup the patient did not report any complain and the uroflow test was similar to a normal urination. From one case report and literature review, the authors suggest a diagnostic and therapeutic strategy for the management of this rare condition.