This study sought to determine whether exercise capacity, self-efficacy, and gross motor skills are associated with moderate-to-vigorous physical activity (MVPA) levels in children, and if these associations differ by congenital heart disease (CHD) type. Medical history was abstracted from chart review. We assessed MVPA levels (via accelerometry), percent-predicted peak oxygen consumption (\(V_{{{\text{O}}_{2} }} ;\) cardiopulmonary exercise test), gross motor skill percentiles (test of gross motor development version-2), and self-efficacy [children’s self-perceptions of adequacy and predilection for physical activity scale (CSAPPA scale)]. CHD patients (n = 137, range 4–12 years) included children with a repaired atrial septal defect (n = 31, mean ± standard deviation MVPA = 454 ± 246 min/week), transposition of the great arteries after the arterial switch operation (n = 34, MVPA = 423 ± 196 min/week), tetralogy of Fallot after primary repair (n = 37, MVPA = 389 ± 211 min/week), or single ventricle after the Fontan procedure (n = 35, MVPA = 405 ± 256 min/week). MVPA did not differ significantly between CHD groups (p = 0.68). Higher MVPA was associated with a higher percent-predicted \(V_{{{\text{O}}_{2} }}\) (EST[95% CI] = 16.9[−0.2, 34] MVPA min/week per 10% increase in percent-predicted \(V_{{{\text{O}}_{2} }} ,\) p = 0.05) and higher self-efficacy (EST[95% CI] = 5.2[1.0, 9.3] MVPA min/week per 1-unit increase in CSAPPA score, p = 0.02), after adjustment for age, sex, and testing seasonality, with no association with CHD type. Higher MVPA was not associated with gross motor skill percentile (p = 0.92). There were no significant interactions between CHD type and percent-predicted \(V_{{{\text{O}}_{2} }} ,\) self-efficacy scores, and gross motor skill percentiles regarding their association with MVPA (p > 0.05 for all). Greater MVPA was associated with higher exercise capacity and self-efficacy, but not gross motor skills.