Purpose: The purpose of this study was to study the relationship between motor competence (MC) and self-esteem in children between 7 and 13 years of age. Methods: This is five years mixed longitudinal study, although only the last two years were included in the analysis. Participants were N = 144 of both sexes (69 girls) divided in 6 cohorts. At baseline the youngest and the oldest cohorts had 4 and 9 years of age respectively. MC was assessed with KTK. Self-esteem and self-worth were assessed with the Portuguese version of Physical Self-Perception Profile for Children and Youth (PSPP-CY). Cross-lagged models were used to find out whether MC predicts self-esteem and self-worth, or the reverse. Linear mixed models were applied. Results: Overall, only self-esteem was predicted by MC across age. Results show that self-esteem had a significant decrease between 7 and 13 years of age (−0.56) and that MC is positively associated with self-esteem (b = 0.006). Conclusions: MC had a mitigating effect on the decrease of self-esteem. Promoting MC during childhood and adolescence might have a positive effect on children's well-being and mental health and prevent them to dropout from physical activities.