Acute exercise reduces postprandial triacylglycerol concentrations ([TAG]) in boys and girls; however, it is not known whether between-sex differences exist in response to exercise. Fifteen boys (mean(SD): 11.8(0.4) years) and sixteen girls (12.1(0.7) years) completed two, 2-day conditions. On day 1, participants rested (CON) or completed 10 × 1 min high-intensity interval runs at 100% maximal aerobic speed with 1 min recovery (HIIR). On day 2, participants consumed a standardised breakfast and lunch over a 6.5-h period during which seven capillary blood samples were collected. Based on ratios of the geometric means (95% CI for ratios), fasting [TAG] was 32% lower in boys than girls (-44 to -18%, ES = 1.31, P < 0.001), and 12% lower after HIIR than CON (-18 to -5%, ES = 0.42, P = 0.003); the magnitude of reduction was not significantly different between the sexes (8% (ES = 0.36) vs. 15% (ES = 0.47), respectively; P = 0.29). The total area under the [TAG] versus time curve was 27% lower in boys than girls (-40 to -10%, ES = 1.02, P = 0.005), and 10% lower after HIIR than CON (-16 to -5%, ES = 0.36, P = 0.001); the magnitude of reduction was similar between the sexes (11% (ES = 0.43) vs. 10% (ES = 0.31), respectively; P = 0.87). The small-moderate reduction in postprandial [TAG] after HIIR was similar between the sexes.