Functional abilities are needed for activities of daily living. In general, these skills expand with age. We hypothesised that, in contrast to what is normally expected, children surviving the Fontan may have deterioration of functional abilities, and that peri-Fontan stroke is associated with this deterioration. All children registered in the Western Canadian Complex Pediatric Therapies Follow-up Program who survived a Fontan operation in the period 1999–2016 were eligible for inclusion. At the age of 2 years (pre-Fontan) and 4.5 years (post-Fontan), the Adaptive Behavior Assessment System-II general adaptive composite score was determined (population mean: 100, standard deviation: 15). Deterioration of functional abilities was defined as ⩾1 standard deviation decrease in pre- to post-Fontan scores. Perioperative strokes were identified through chart review. Multivariable logistic regression analysis determined predictors of deterioration of functional abilities. Of 133 children, with a mean age at Fontan of 3.3 years (standard deviation 0.8) and 65% male, the mean (standard deviation) general adaptive composite score was 90.6 (17.5) at 2 years and 88.3 (19.1) at 4.5 years. After Fontan, deterioration of functional abilities occurred in 34 (26%) children, with a mean decline of 21.8 (7.1) points. Evidence of peri-Fontan stroke was found in 10 (29%) children who had deterioration of functional abilities. Peri-Fontan stroke (odds ratio 5.00 (95% CI 1.74, 14.36)) and older age at Fontan (odds ratio 1.67 (95% CI 1.02, 2.73)) predicted functional deterioration. The trajectory of functional abilities should be assessed in this population, as more than 25% experience deterioration. Efforts to prevent peri-Fontan stroke, and to complete the Fontan operation at an earlier age, may lead to reduction of this deterioration.