Current studies on the incidence of arrhythmias after the intra-atrial lateral tunnel (ILT) Fontan operation and the extra-cardiac conduit (ECC) Fontan operation are limited, with controversial results. This systematic review aimed to compare the prevalence of arrhythmias in patients who underwent ECC or ILT Fontan. Relevant studies comparing the incidence of arrhythmias and pacemaker implantation in ILT with ECC were identified through a literature search using MEDLINE, EMBASE, and the cochrane central register of controlled trials. The outcome measures included baseline characteristics, early (≤30 days) and late (>30 days) arrhythmias and pacemaker implantation. 16 publications involving 3499 patients were included. In the meta-analysis, although the overall risk of early arrhythmias was lower for the ILT group, statistically, no significant difference was observed (odds ratio [OR] 0.78; 95% confidence interval [CI] 0.61–1.01; p = 0.06). Similarly, there was no significant difference between the two cohorts in the incidence of postoperative permanent pacemaker therapy (OR 1.36; 95% CI 0.86–2.14; p = 0.19). However, we found significantly increased incidence of late arrhythmias in ILT group compared with ECC group (OR 1.96; 95% CI 1.64–2.35; p < 0.01). Although our systematic review and meta-analysis suggested that there was no significant difference in early arrhythmias and in pacemaker implantation between the ILT and ECC groups, ECC procedure could significantly lower the risk of late arrhythmias after Fontan surgery. Given that some limitations cannot be overcome, well-designed randomized controlled trials are needed to confirm our findings.