The objective of this study was to evaluate the active lifestyle capacity (daily physical activity, strength, flexibility, body composition) of children after the Fontan procedure; hypothesized to be lower than healthy peers. Participants (n = 64, 25 females) were 9.0 ± 1.7 years of age (range 6.0–11.7 years). Fontan completion occurred at 3.3 ± 1.4 years of age (5.7 ± 2.0 years prior). Canadian Health Measures Survey protocols assessed aerobic endurance (paced walking up/down steps), strength (handgrip), flexibility (sit and reach), body composition (body mass index), and daily moderate-to-vigorous physical activity (7-day accelerometry). Difference scores compared participant data to published norms (t tests). Linear regression evaluated age/gender/demographic factor associations. Children after Fontan had strength scores similar (mean difference 1.1 kg) to their peers were less likely to be obese (mean difference of body mass index = 1.1 ± 2.5, p = 0.001) and performed 50 min of moderate-to-vigorous activity (MVPA) per day (12 ± 17 min/day below healthy peers, p < 0.001). Estimated peak endurance (61 % of expected) and flexibility (64 % of expected) were lower than peers (p < 0.001). Almost all (60/63) participants demonstrated the capacity to perform at least 20 min of MVPA per day. Difference from norms was smaller among children younger at Fontan completion (4 ± 2 min/year) and taking antithrombotic medication (7 ± 18 and 22 ± 17 min/day for taking/not taking, respectively). Children after Fontan demonstrate the capacity for the daily physical activity associated with optimal health. They have similar strength and good body composition. We recommend that children after Fontan be counselled that they can successfully participate in healthy, active lifestyles and physically active peer play.