Physical fitness, intelligence and academic achievement are being studied from a multidisciplinary perspective. In this line, studies to advance our understanding of intelligence and academic achievement could be relevant for designing school-based programs. Our study analyzed the relationship between components of physical fitness including cardiorespiratory fitness, muscular strength and flexibility and general intelligence and academic achievement in adolescents. We recruited 403 adolescents (53.6% boys) with a mean age of 13.7 ± 1.2 years from a secondary school in Spain with a medium socioeconomic status, during the 2015/2016 school year. Cardiorespiratory fitness was assessed by the 20-m shuttle run, muscular strength with the standing long jump test and flexibility with the sit-and-reach test. General intelligence was measured by both the D48 and the Raven tests. School grades were used to determine academic achievement. Linear regression analyses showed that cardiorespiratory fitness was positively associated with intelligence in both the D48 (all β ≥ 0.184, p ≤ 0.016) and the Raven tests (all β ≥ 0.183, p ≤ 0.024). Muscular strength, flexibility and overall fitness were not associated with intelligence (all β ≤ 0.122, p ≥ 0.139). Cardiorespiratory fitness, muscular strength and flexibility were positively associated with academic achievement (all β ≥ 0.089, p ≤ 0.038), except muscular strength, which was not significantly associated with Spanish language or mathematics, (all β ≤ 0.050, p ≥ 0.200). Overall, cardiorespiratory fitness was positively associated with intelligence and academic achievement.