<p>Whether atrial isomerism (AI) is associated with impaired long-term outcomes in Fontan circulation remains highly controversial, partially owing to the associated complex cardiac malformation. This study aimed to compare both early and late outcomes between Fontan patients with and without AI. 323 patients with (n = 56) or without (n = 267) AI undergoing Fontan procedure at our institution from January 2004 to December 2021 were retrospectively reviewed. We matched AI and non-AI Fontan patients in a 1:2 ratio using propensity score matching and compared their outcomes. The primary endpoints were death or transplantation and a composite of Fontan failure. Postoperative mean or maximum vasoactive-inotropic scores in hospital in the matched AI group were significantly higher than in the matched non-AI group (p &lt; 0.05). The 5-year and 10-year transplantation-free survival rates were estimated to be 85.9% and 81.6% in the matched AI group, significantly lower than 96.2% and 91.2% in the matched non-AI group, respectively (p &lt; 0.05). The estimated freedom from Fontan failure at 5 years and 10 years was 85.9% and 70.1% in the matched AI group, significantly lower than 92.4% and 89.7% in the matched non-AI group, respectively (p &lt; 0.05). Cumulative incidence of arrhythmia and atrioventricular valve regurgitation ≥ moderate was similar between the two groups. In Cox multivariable analysis, AI (HR, 2.120; 95%CI, 1.107–4.060) was identified as an independent risk factor for Fontan failure. Both the early and late outcomes of Fontan circulation with AI were inferior compared with those without AI. AI was an independent risk factor for postoperative Fontan failure.</p>