Previous studies have suggested that submaximal energy expenditure relative to body mass during weight-bearing exercise may be greater in boys compared to girls. This two-part study examined a) gender-related five-year longitudinal changes in submaximal walking economy and b) gross, net, and delta muscle work efficiency during submaximal cycle exercise in a cross-sectional analysis of boys and girls. In the longitudinal study, the influence of pre-exercise metabolic expenditure, stride frequency, and substrate utilization (by RER) on changes in economy were examined. During the five years, mean VO2 per kg during submaximal treadmill walking (measured at 8% slope, 3.25 mph) decreased 16% in girls and 13% in boys (p > 0.05 for gender). Likewise, no significant gender differences were observed in decline of stride frequency over time. RER values were similar between sexes except in the final two years when girls had significantly greater values than the boys. No gender-related differences were observed in any measure of muscle work efficiency. This study failed to reveal significant gender differences in utilization of energy during submaximal exercise in children.