Background <p>Aquatic exercise may be a feasible strategy for improving cardiovascular health in children with obesity, but evidence comparing aquatic high-intensity interval training (aHIIT) and aquatic moderate-intensity continuous training (aMICT) remains limited. This pilot randomized controlled trial compared the effects of 8 weeks of aHIIT and aMICT on endothelial function, estimated cardiorespiratory fitness, central hemodynamic indices, arterial stiffness, and anthropometric indicators in school-aged children with obesity.</p> Methods <p>Thirty-three children with obesity were randomized to the aHIIT group (<i>n</i> = 11), aMICT group (<i>n</i> = 11), or non-exercise control group (<i>n</i> = 11). The two aquatic exercise groups trained 3 days/week for 8 weeks. The aHIIT protocol consisted of 10 × 30-s high-intensity aquatic exercise (such as freestyle swimming or freestyle kicking) bouts at 80%-90% HRmax, separated by 60-s recovery intervals, whereas the aMICT protocol consisted of two 15-min continuous breaststroke bouts at 60%-70% HRmax, separated by a 5-min recovery interval. Brachial artery flow-mediated dilation (FMD) was used as the principal vascular outcome. Central hemodynamic indices were assessed using applanation tonometry, and estimated VO_2max was obtained from the 20-m shuttle run test. Intervention effects were analyzed using two-way repeated-measures ANOVA, with the group × time interaction used as the primary test for differential intervention effects.</p> Results <p>Significant group × time interactions were observed for estimated VO_2max, FMD, AIx, and AIx@HR75. Estimated VO_2max increased in both aquatic exercise groups compared with the control group. FMD improved in both exercise groups, with a greater increase observed after aHIIT. AIx and AIx@HR75 showed favorable changes after aMICT. No significant group × time interactions were observed for resting blood pressure, SEVR, ABI, cfPWV, or baPWV.</p> Conclusion <p>This pilot trial suggests that both aHIIT and aMICT may improve estimated cardiorespiratory fitness in school-aged children with obesity. aHIIT may be associated with greater improvement in brachial artery endothelial function, whereas aMICT may have favorable effects on selected wave-reflection-related indices. However, these findings should be interpreted cautiously because of the small sample size, indirect estimated VO_2max estimation, lack of maturation assessment, and unmatched exercise workload.</p> Trial registration <p>Chinese Clinical Trial Registration, ChiCTR2400080687.05/02/2024.</p>