The objective of this study is to meta-analyse the published literature comparing outcomes after open (ONF) versus laparoscopic Nissen fundoplication (LNF) for gastro-oesophageal reflux disease in children. Electronic databases were searched from January 1993 to October 2009. A systematic review was performed to obtain a summative outcome. Six comparative studies were analysed. There were 466 patients in the laparoscopic group and 255 in the open group. There was no significant difference in operative time between LNF compared with ONF (p = 0.35). Children stayed in hospital for less time after undergoing LNF compared with ONF [random effects model: SMD = 0.93, 95% CI (0.41, 1.44), z = 3.53, p < 0.01]. Children feed earlier after LNF [random effects model: SMD = 4.13, 95% CI (1.00, 7.27), z = 2.58, p < 0.001] and had less morbidity [fixed effects model: RR = 3.22, 95% CI (1.98, 5.25), z = 4.71, p < 0.01; random effects model: RR = 2.90, 95% CI (1.49, 5.66), z = 3.12, p < 0.01]. No difference in recurrence at 12 months was highlighted (p = 0.29). In conclusion, the laparoscopic Nissen's fundoplication in children may be considered a safe and effective alternative to open surgery; however, careful case selection is required.