Aim: The aim of this study is to report the experience with minimally invasive surgery (MIS) in neonates with congenital malformations in a tertiary care pediatric hospital. Materials and Methods: Design: descriptive study. All neonates undergoing MIS from 2013 to 2018 were included in the study. Perinatal data, characteristics of surgery, type and duration of analgesia, postoperative mechanical ventilation duration, postoperative hospitalization, and postoperative morbidity and mortality surgery-related rates were recorded. Results: Seventy-one neonates were included. Gestational age and weight at surgery ranged from 24 to 41 weeks and from 1350 g to 4830 g, respectively. Procedures performed were esophageal atresia/tracheoesophageal fistula repair, congenital diaphragmatic hernia repair, diaphragmatic plication, fundoplication/gastrostomy, intestinal atresia repair, and pancreatectomy. The median follow-up period was 14 months. Five neonates (7%) were converted to open, for surgical difficulties. Nine (12.6%) neonates had intraoperative complications, with decreased oxygen saturation as the most common complication. The median duration of analgesia and postoperative mechanical ventilation was 3 days in most procedures. The morbidity and mortality rates were 36.6% and 2.8%, respectively. Conclusions: In this first experience with MIS in neonates, the duration of analgesia and hospitalization was shorter for some procedures. However, intraoperative and postoperative complications were still high, which was possibly attributed to the learning curve. Thus, it is expected that the frequency of the complications presented in this study will be reduced in future.