Non‐invasive assessment of central arterial pulse wave augmentation has been proved to be useful in predicting cardiovascular adverse events. Previous studies have shown that prepubescent girls had greater central augmentation pressure compared with height‐matched boys. This study sought to investigate which factors contribute to the body height‐independent sexual differences in central arterial wave reflection observed in childhood. This cross‐sectional study involved 819 children and adolescents (6‐18 years of age) of both sexes. Phenotypes of central haemodynamic were obtained by radial applanation tonometry. Heart rate corrected augmentation index (Aix@75) was greater in girls compared with boys (2.9 ± 10.7 vs. ‐1.7 ± 12.9%, p <0.001) as well as the central augmented pressure (cAP) (1.3 ± 3.3 vs. 0.1 ± 3.8 mmHg, p <0.001), even adjusting for age, heart rate and body height. Left ventricular ejection duration (ED) was longer (320 ± 26 vs. 314 ±24 ms, p = 0.004) and time to inflection point (Tr) was shorter in girls (139 ± 14 vs. 141 ± 21 ms, p = 0.014). The reduction of Aix@75 with increasing body height was steeper in boys (‐0.499 ± 0.030 vs. ‐0.428 ± 0.036%/cm, p < 0.001) as well as the reduction of cAP with increasing body height (‐0.108 ± 0.010 vs. ‐0.066 ± 0.013 mmHg/cm, p <0.001). Body height‐independent sexual differences observed in the pulse wave reflection indices from early adolescence were mediated by different timing of forward and reflected pressure waves. This article is protected by copyright. All rights reserved.