Heart rate recovery (HRR) is an indicator of all-cause mortality in children and adults. We aimed to determine the effect of adiposity and Prader-Willi Syndrome (PWS), a congenital form of obesity, on HRR. Sixteen children of normal weight (NW = body fat % ≤85th percentile, 9.4 ± 1.1 y), 18 children with obesity (OB = body fat % >95th percentile, 9.3 ± 1.1 y), and 11 PWS youth (regardless of body fat %; 11.4 ± 2.5 y) completed peak and submaximal bike tests on separate visits. HRR was recorded one minute following peak and submaximal exercises. All groups displayed similar HRR from peak exercise, while NW (54 ± 16 beats) and OB (50 ± 12 beats) exhibited a significantly faster HRR from submaximal exercise than PWS (37 ± 14 beats). These data suggest that excess adiposity does not influence HRR in children, but other factors such as low cardiovascular fitness and/or autonomic dysfunction might be more influential.