Dysuria with lower abdominal pain is a common presentation for a urinary tract infection (UTI), and diagnosis is based on symptoms together with a urinalysis and urine culture suggestive of infection. UTI is uncommon in circumcised males who are not sexually active. When urine culture is negative, alternate diagnoses including, but not limited to, gastroenteritis, severe constipation, appendicitis, or epididymitis need to be considered. In patients with a known urologic history of proximal hypospadias and/or disorders of sexual development, rarer diagnoses also need to be considered. This paper reports the case of a 13-year-old male with a remote history of proximal hypospadias repair, who presented with nonspecific lower urinary tract symptoms. Initially he was treated for UTI. However, urine cultures remained negative despite persistent urinary tract symptoms. On further workup, he was found to have an enlarged and infected prostatic utricle. This report illustrates the importance of considering an enlarged prostatic utricle in the differential diagnoses of patients with chronic lower urinary tract symptoms and a history of hypospadias. Additionally, this case highlights the utility of magnetic resonance imaging (MRI) in clarifying lower urinary tract anatomy in cases where ultrasound is inconclusive.