Background: The practice of physical activity (PA) plays an important role in achieving an active-healthy lifestyle. Several authors have focused their studies on the relationship between motor competence (MC) and physical activity (PA). Stodden et al. proposed a conceptual model, where they postulated the existence of a positive and significant relationship between the two variables and that there are mediating variables that play a critical role in this relationship as perceived motor competence (PMC). Aims: Therefore, the purpose of this research is to provide empirical evidence to support the conceptual model. The aim is to examine the association of PMC and MC with PA and to determine whether PMC is a mediator of the association between MC and PA in Basque adolescents. Methods: 897 students between 12 and 16 years old from the Basque Country (Spain) participated in this study. The SPORTCOMP battery was used to assess motor competence and the AMPET-R questionnaire was applied to measure the PMC. To know the level of PA participants were asked how many days per week they performed physical activity, considering physical activity to include any sport activity, organized or unorganized, that meets the conditions of a minimum duration of 60 min medium and vigorous intensity. A descriptive, correlational and direct/indirect effect approach was used, using the PROCESS macro for Statistical Package for the Social Sciences (SPSS). Results: The results highlight that, on the one hand, PMC significantly correlates with both MC and PA and, on the other hand, it is corroborated that PMC is a mediator variable in the relationship between MC and PA. Conclusion: The mediation role of the PMC in the association between MC and PA raises the necessity not only to improve motor skills but also to provide successful experiences that allow adolescents to build a competent image of themselves that will contribute to the achievement and maintenance of an active lifestyle.