Background: Urachal cysts are uncommon congenital anomalies that usually remain asymptomatic until complicated by infection. Presentation as acute small bowel obstruction is exceedingly rare and poses a diagnostic challenge.

Case Presentation: A 15-year-old boy with Arnold–Chiari type II malformation, repaired meningomyelocele, ventriculoperitoneal shunt, and neurogenic bladder presented with fever, lower abdominal pain, abdominal distension, bilious vomiting, and constipation. Contrast-enhanced computed tomography demonstrated a 7 × 7 cm infected urachal cyst arising from the bladder dome with surrounding inflammatory changes causing acute small bowel obstruction. Emergency diagnostic laparoscopy was attempted but converted to an open procedure because of dense inflammatory adhesions. Complete excision of the infected urachal cyst with en bloc partial cystectomy was performed. Histopathological examination confirmed an infected urachal cyst without evidence of malignancy. The patient recovered uneventfully and remained asymptomatic on follow-up.