Pneumoperitoneum in a neonate is a serious condition for which bowel perforation is indicated in most cases. Because the transdiaphragmatic air dissection could occur in some ventilated neonates without peritonitis, making the right diagnosis is sometimes difficult, and exploratory laparotomy is often necessary. Here, we report the first case of neonatal pneumoperitoneum caused by a perforated Meckel's diverticulum in which diagnostic laparoscopy was useful in achieving minimal access surgery. Using a multiuse single-site port on the umbilicus could enable the extraction of a certain length of a small intestine with good cosmetic results. This method would decrease the hurdles of early surgical interventions for the suspected perforation of unknown aetiology and shorten the fasting period, which is beneficial for the neurodevelopment of small neonates.