Abstract Background/Purpose Whether laparoscopic surgery is superior to open surgery in the repair of congenital duodenal obstruction remains controversial. The objective of this study is to systematically review the literatures which compare the outcomes of these two operative approaches. Methods A systematic review of the studies comparing these two surgical approaches since 2000 was carried out. Results Four retrospective cohort studies compromising 180 patients were eligible for analysis. Duodenal atresia was the most common diagnosis (62.3%). Overall, there were no statistically significant differences in terms of operative duration (SMD: 0.75, 95% CI: 0.46–1.04), ventilator dependence (SMD: 0.04, 95% CI: − 0.22 – 0.29), time to initial enteral feeding (SMD: 0.12, 95% CI: − 0.14 – 0.38), time to full enteral feeding (SMD: 0.18, 95% CI: − 0.15 – 0.50) and hospital stay (SMD-0.03, 95% CI: − 0.29 – 0.22). The overall incidences of anastomotic complications in laparoscopic vs open groups were 4.4% vs 1.8%. Two cases of missed distal pathology were reported in the laparoscopic group. Conclusions Laparoscopic surgery is feasible in the repair of CDO. Study with larger sample size is needed for further analysis to examine whether open or laparoscopic approach is superior. Meanwhile, it is still safe to practice laparoscopic repair of CDO in skilled surgeons with attention to the possibility of distal pathology.