We studied the associations of overweight (OW, BMI ≥85th percentile) and physical activity (PA) with physical fitness in adolescents. The nationally representative sample was 1120 boys and 1146 girls, aged 15–16 years. Height and weight were self-reported. The level of PA was based on self-reported frequency and duration of sweating during organized and non-organized activity. Fitness was measured by sit-ups, sit-and-reach, five-jump, back-and-forth jumping, ball skills, coordination and endurance shuttle run tests. The fitness index was calculated as the mean of z-scores for individual tests. The prevalence of OW was 17.3% in boys and 11.8% in girls. The main effect of PA (in analysis of variance) on all fitness tests was significant (P≤0.005). The main effect of OW was significant (P<0.002) for all tests, except for sit-and-reach. According to linear regression models, the association between PA and fitness was stronger than that between OW and fitness. Sit-ups, endurance shuttle-run and fitness index showed the strongest association with PA (standardized β coefficients 0.31–0.49). OW was not associated with sit-and-reach test (coefficient 0.04) and only weakly with the ball skills test (coefficients −0.10 to −0.12). In conclusion, OW had the most negative association with cardiorespiratory and muscle endurance, and explosive power tests.