Studies on the arrhythmia incidence in the Fontan population, especially comparing intracardiac (IC) and extracardiac (EC) Fontan, are limited, with inconsistent findings. This meta-analysis aims to compare arrhythmia risk in EC and IC Fontan patients. Eligible studies comparing arrhythmia outcomes following different Fontan procedures, including EC conduit (ECC), lateral tunnel (LT), and classic Fontan, were identified through a systematic search of the PubMed, Cochrane Library, EMBASE, and Google Scholar databases from 2016 to 2025. Random-effects meta-analysis was performed to pool odds ratios (ORs). A subgroup analysis based on follow-up duration and a restricted analysis comparing ECC versus LT were conducted to explore heterogeneity. Twelve publications with 6280 patients were included in the final analysis. In our systematic review and meta-analysis, the EC Fontan was associated with significantly lower odds of arrhythmia compared to the IC Fontan (OR = 0.38, 95% confidence interval [CI]: 0.27–0.52, P < 0.001), with substantial heterogeneity (I 2 = 74%). In a restricted analysis comparing only ECC with LT, the association remained significant (OR = 0.52, 95% CI: 0.39–0.69; P < 0.001). EC Fontan is linked to a lower observed arrhythmia burden compared to IC Fontan. However, this finding should be interpreted cautiously, as the observed effect may partly reflect the higher arrhythmia burden in classic Fontan, as well as differences in surgical era and follow-up duration. Given the persistent risk of arrhythmia in all Fontan patients, individualized management and long-term surveillance are essential. © 2026 Annals of Pediatric Cardiology.