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This study aimed to evaluate the feasibility and efficacy of laparoscopic management in neonates diagnosed with congenital gastric muscular layer defects and gastric perforation. A retrospective analysis was conducted on four male neonates (median gestational age: 36.79 weeks; median birth weight: 2460 g) who underwent laparoscopic repair at Shanxi Provincial Children’s Hospital between January 2022 and October 2024. All neonates presented with symptoms of vomiting, feeding intolerance, and abdominal distension, with preoperative imaging confirming pneumoperitoneum. Laparoscopic surgery was successfully completed in all cases without conversion to open surgery. The median operative time was 102 min, and no surgery-related complications such as anastomotic leakage or hemorrhage were observed. One neonate was transferred to the department of internal medicine due to postoperative feeding difficulties, failure, and persistent oxygen dependence. The median hospital stay was 27.5 days. At the 6-month postoperative follow-up, three neonates exhibited satisfactory growth and development, while one exhibited mild growth delay. Our findings indicate that laparoscopic repair offers significant advantages, including mitigated surgical trauma, quicker recovery, and lower incidence of intestinal adhesion. Provided that surgical indications are strictly assessed and the surgeon possesses proficient laparoscopic skills, it is feasible for specialized surgeons to manage this disease using laparoscopy.