Purpose: To analyze the interrelationships among motor coordination, body fat, and physical activity in adolescent boys. Methods: A total of 69 boys aged 12–14 years were recruited. Motor coordination was assessed using the Körperkoordinationstest für Kinder. Correlations (bivariate and partial) and mediation analysis were used to examine the interrelationships among the selected variables. Results: Body fat was significantly correlated with global motor coordination, walking backward (Motor Quotient 1), and one-legged hopping (Motor Quotient 2) scores with and without controlling for physical activity level. On the other hand, physical activity level was significantly correlated with global motor coordination and Motor Quotient 2 scores only in bivariate analyses (without controlling for body fat). Mediation analysis revealed that body fat percentage was not significantly related to physical activity. Conclusions: Correlations between motor coordination and physical activity can be influenced by body fat in adolescent boys. However, both body fat and physical activity were not mediator variables. Perhaps there are other complementary mechanisms that mediate the interrelationships among motor coordination, body fat, and physical activity in adolescent boys.