The purpose of this study was to retrospectively compare the short-term outcomes of robotic- (RAD) and laparoscopic-assisted duodenal diamond-shaped anastomosis (LAD) in neonates. Neonates who underwent RAD (n = 30) or LAD (n = 38) between January 2019 and December 2022 were analyzed retrospectively. Major patient data were collected, including preoperative, intraoperative, and postoperative information. All patients were neonates below the age of 30days weighing 4kg. Thirty (44.1%) neonates underwent RAD and 38 neonates (55.9%) underwent LAD. Compared to the LAD group, the RAD group had a shorter intra-abdominal operation time (RAD, 60.0(50.0 ~ 70.0)min; LAD, 79.9(69.0 ~ 95.3)min; p < 0.001). There were no significant differences in immediate and 30-day complications between the two groups. RAD is safe and effective in neonates. Compared to traditional LAD, RAD showed comparable results.