The aim was to examine the bidirectional association between cardiorespiratory fitness (CRF) and fatness in a 2‐year longitudinal study conducted in young people. A total of 1082 children (512 females) and 727 adolescents (342 females) with complete data at baseline and follow‐up were included. CRF was determined by the 20‐m shuttle run test. Height and weight were measured, and body mass index and fat mass index (kg/m2) were calculated. Triceps and subscapular skinfolds were assessed to compute body fat percentage. Bidirectionality was tested by including CRF and each fatness index as exposures and outcomes, alternatively, in different regression models. CRF was prospectively associated with fatness index levels (ß from −0.186 to −0.528; P < .001), remaining significant in children after adjusting for baseline fatness indices. Fatness indices were prospectively associated with CRF (ß from −0.207 to −0.479; P < .001), with no substantial changes observed in children and female adolescents when baseline CRF was considered. Changes in CRF were prospectively associated with several fatness indices, regardless of body fatness at baseline (ß from −0.062 to −0.220; P < .05). Body fatness changes were associated with future CRF levels, independently of baseline CRF, especially in children of both sexes and male adolescents (ß from −0.079 to −0.260; P < .05). Overall, a bidirectional association was observed between CRF and fatness in children and adolescents. The attainment of optimal CRF and fatness levels in early ages should be promoted since it could result in favorable future fatness and CRF levels, respectively, which are two key determinants of health status.