Motor competence has been shown to predict health-related physical fitness (HRPF) components in youth, but there is indeterminate evidence for the reverse path. Even less is known about the specific relationship between motor competence and flexibility. Our aims in this study were to analyze the relationship between flexibility and motor competence among adolescents; and, secondarily, to examine the relationships between motor competence and other HRPF components (body composition and musculoskeletal fitness). We conducted a longitudinal study (14-months follow-up) with two measurement points of 128 participants (55.5% girls; 45% boys) aged 12–13 years at baseline. We assessed HRPF components at the first time point and determined motor competence at the second time point. We assessed HRPF in terms of body composition (body fat percentage), musculoskeletal fitness (sit-up test), and flexibility (sit and reach). We determined motor competence using the Körperkoordinationstest für Kinder (KTK). We employed multivariate analyses of variance (MANOVA) to examine the effect of HRPF on motor competence through three models, in which each HRPF component was considered an independent variable. Sex, age, physical activity, and body mass index (BMI) z-scores were considered confounders. In our crude models all HRPF components significantly affected motor competence. In adjusted models, flexibility ( p = .002) and body composition ( p < .001) significantly affected motor competence. Overall, these results supported the assumptions that HRPF components are related to motor competence in adolescence, and that flexibility can affect motor competence in young people.