Introduction: The influence of socioeconomic status on health-related fitness is not clear. Aim: To examine the influence of socioeconomic status on health-related fitness in adolescents. Methods: A total of 3,259 adolescents (15.0 ± 1.3 y) from the Healthy Lifestyle in Europe by Nutrition in Adolescence Cross-Sectional Study (HELENA-CSS) participated in the study. Socioeconomic status was assessed by the family affluence scale (FAS). Speed-agility, muscular strength and cardiorespiratory fitness were assessed. Covariates included total body fat, physical activity and pubertal status. Results: Adolescents with high FAS had significantly higher fitness levels than their peers of lower FAS categories except for speed-agility and handgrip in boys. Overall, the associations observed presented a medium to large effect size. Conclusion: These results suggest that socioeconomic status is positively associated with physical fitness in European adolescents independently of total body fat and habitual physical activity.