This meta-analysis was designed to determine the effect of an intracardiac lateral tunnel (ILT) versus an extracardiac conduit (ECC) on patients undergoing a Fontan procedure. A search of the literature in PubMed, Embase, China Academic Literature, and Wanfang databases yielded 23 studies comprising approximately 1000 patients for analysis. There were statistically significant differences between ILT and ECC in the frequency of early sinus node dysfunction, early total arrhythmias, late supraventricular tachycardia, late sinus node dysfunction, late total arrhythmias, and need for pacemaker. By contrast, no statistically significant differences between the two methods were found in takedown, protein-losing enteropathy, thromboembolic events, early supraventricular tachycardia, early mortality, and total mortality. We conclude that an ECC confers some advantages over an ILT, although the underlying mechanism remains unclear.