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A late preterm male baby with antenatally diagnosed left-sided congenital diaphragmatic hernia (CDH) was delivered electively at 36 weeks of gestation. He remained stable until day 2 of life, when he developed severe persistent pulmonary hypertension secondary to sepsis, including persistent Candida sepsis, delaying CDH repair. On day 13, he developed sudden abdominal distension, and radiography confirmed pneumoperitoneum without pneumothorax. Primary peritoneal drainage released a gush of air, following which exploratory surgery was performed. Intraoperative findings revealed two separate small bowel perforations that were resected and anastomosed along with CDH repair. This case highlights one of the first reported instances of true surgical pneumoperitoneum secondary to bowel perforations in a neonate with CDH, unlike previously described cases where pneumoperitoneum was attributed to pulmonary air leaks or gastric perforation.