The aim of this study was to investigate the mediating role of motivation in the relationship between coaches’ emotional intelligence and the academic adjustment of student athletes. The research involved 317 student athletes (168 males and 149 females, aged 14 to 18) from various sports disciplines, including basketball, football, volleyball, and track and field. Standardized questionnaires were utilized to assess the emotional intelligence of coaches, motivation, and academic adjustment. Statistical analysis was conducted using the Macro Process version 4 software. The results indicated a positive correlation between coaches’ emotional intelligence and motivation (r = 0.42, p < 0.001) as well as academic adjustment (r = 0.36, p < 0.001). Furthermore, motivation was positively correlated with academic adjustment (r = 0.47, p < 0.001). Notably, motivation significantly mediated the relationship between coaches’ emotional intelligence and academic adjustment (95% CI [0.20, 0.08], b = 0.13). These findings underscore the importance of coaches’ emotional intelligence in enhancing the academic adjustment of student athletes through increased motivation, highlighting the need for emotional and motivational support in both educational and athletic environments. Additionally, the results can inform the development of coach training programs and school sports policies aimed at fostering the growth of student athlete communities.