Obesity has been associated with poor academic achievement, while cardiorespiratory fitness (CRF) has been linked to academic success. Purpose: To investigate whether CRF is associated with academic performance in Brazilian students, independently of body mass index (BMI), fatness and socioeconomic status (SES). Methods: 392 5th and 6th grade students (193 girls) (12.11 ± 0.75 years old) were evaluated in 2012. Skinfold thickness measures were performed, and students were classified according to BMI-percentile. CRF was estimated by a 20-meter shuttle run test, and academic achievement by standardized math and Portuguese tests. Multiple linear regression analyses were conducted to explore the association between academic performance and CRF, adjusted for SES, skinfold thickness or BMI-percentile. Results: Among girls CRF was associated with higher academic achievement in math (β = 0.146;p = .003) and Portuguese (β = 0.129;p = .004) in crude and adjusted analyses. No significant association was found among boys. BMI was not associated with overall academic performance. There was a weak negative association between skinfold thickness and performance in mathematics in boys (β =- 0.030;p = .04), but not in girls. Conclusion: The results highlight the importance of maintaining high fitness levels in girls throughout adolescence a period commonly associated with reductions in physical activity levels and CRF.