Physical activity (PA) has shown to be promising in the increase of cardiorespiratory fitness in children and adolescents. Nevertheless, current evidence lacks knowledge concerning the independent and combined effect of active commuting and PA on cardiorespiratory fitness (CRF). The aims of the current study were to examine the associations of CRF with PA and the mode of commuting to school separately as well as to explore the associations of CRF with the combination of PA and mode of commuting to school. A total sample size of 2518 students (13.0 +/- 2.1 years old) from Balearic Islands (Spain) aged between 10 and 16 years old participated in this cross-sectional study. The data regarding PA patterns and the mode of commuting to school were collected with a self-reported questionnaire. Cardiorespiratory fitness was measured by means of a 20-m shuttle run test. The multilevel models showed associations between CRF and PA in adolescents, but not in children (beta = 0.002, p = 0.076 in children; beta = 0.004, p = 0.049 in adolescents). However, CRF was not associated with the mode of commuting in either children or adolescents (all, p > 0.050). Adolescents who complied with the PA recommendations had better CRF compared with those who did not, regardless of how they commuted to school (p = 0.053 and p = 0.052). In conclusion, our results show the relevance of the intensity of daily PA in understanding the associations between CRF and active commuting in adolescents.