We assessed the association between school time and physical fitness in adolescents. The study included 2,024 adolescents, aged 12.5-17.5 years, who participated in the Healthy Lifestyle in Europe by Nutrition in Adolescence study. Health-related physical fitness components were assessed using the physical fitness tests battery. Cardiovascular risk was categorized using the sex-specific cut-offs for a healthy cardiorespiratory fitness level in adolescents proposed by FitnessGram®. School time was classified as short or long. Multivariate analysis accounted for confounding factors such age, sex, body mass index, time spent in moderate to vigorous physical activity, pubertal status, and parents' educational level. Cardiorespiratory fitness was higher in adolescents with a long school time than in those with a short school time (42.0 ± 7.6 vs 40.7 ± 7.2 mL.kg.min, respectively; < 0.05). The percentage of adolescents at cardiovascular risk in adulthood was higher in the short than in the long time group (45.2% vs 31.7%, respectively) ( < 0.05). These findings suggest that a long school day is associated with higher cardiorespiratory fitness in adolescents and that school time should be considered in interventions and health promotion strategies.