This cross-sectional study analyzed the relationship between socioeconomic status (SES, rurality, and both academic achievement (reading, mathematics, and science grades) and physical fitness metrics (BMI, waist circumference, SRT phases, VO2max, flexibility, standing long jump, and arm flexion) in 11,981 eighth-grade students (50% female, mean age 14.51 ± 1.00) from the 2013 Chilean National Physical Education Survey (SIMCE). Linear transformation converted academic scores to the 1–7 Chilean grade scale. Pearson correlations and ANOVA tests (with Bonferroni post-hoc) were performed on Python. Strong positive correlations were found between SES and academic grades (r = 0.56–0.70, p < 0.01), whereas rurality showed negative correlation with math and science performance (p < 0.05). Physical performance showed minimal correlation with SES or rurality, but notable gender differences emerged, particularly in flexibility and jump tests. These findings underscore the role of SES in academic success, while rurality has a subtler effect. Physical performance disparities are better explained by biological sex than social factors. We advocate for equity-focused educational and physical fitness interventions, especially in rural and low-SES populations. Longitudinal studies are needed to explore causal pathways and optimize resource allocation in schools.