The aims of this study were (1) to examine the associations between self-reported health-related quality of life (HRQoL), health-related physical fitness (cardiorespiratory fitness, muscular strength, and speed-agility), and mode of commuting to and from school in Spanish children, and separately by gender and (2) to analyse the difference in cardiorespiratory fitness by mode of commuting to and from school by gender. We conducted a cross-sectional analysis that included 415 children aged 8.47 ± 0.36 years from 14 schools in Granada, Spain. The HRQoL outcome was assessed using the valid and reliable KINDL-R questionnaire, which covers six life dimensions, children's physical fitness was assessed using the ALPHA fitness test battery, and while commuting to and from school was assessed using the valid, reliable, and feasible 'Mode and Frequency of Commuting To and From School Questionnaire'. Cardiorespiratory fitness was positively correlated with all dimensions of HRQoL in boys, whereas higher muscular strength (standing long jump) was positively correlated with the emotional wellbeing dimension in girls. In addition, boys who actively commute to school (walking) presented better cardiorespiratory fitness. Moreover, children who actively commuted to school (walking) presented better scores for the emotional wellbeing, family, and school dimensions, as well as total scores (both, p < .05) of HRQoL. In our study, HRQoL was positively correlated with cardiorespiratory fitness in boys (all dimensions), whereas muscular strength (standing long jump) was positively correlated with the emotional wellbeing dimension only in girls. Active commuting to and from school was associated with higher levels of cardiorespiratory fitness, school dimension, and KINDL-R total score. Improving cardiorespiratory fitness might be especially useful to improve HRQoL in children, and vice versa.