Provision of equitable access to university education is the primary goal of pre-university education. Academically weak students stand to benefit more from pre-university program. However, available literature on effectiveness of the program revealed that high percentage of students still fail pre-university courses. Although the role of psycho-emotional factors on student academic performance has been highlighted, mechanism through which psycho-emotional factors impact on academic performance of pre-university science students is still not clear to offer adequate insights for proper intervention program. Therefore, we examined the pre-university students' academic performance in sciences in relation to Emotional Intelligence (EI) (Interpersonal EI and Intrapersonal EI) and Self-directed Learning (SDL). Specifically, a correlational study design was conducted to measure and gauge the level of relationships amongst Interpersonal EI, Intrapersonal EI, SDL and academic performance of pre-university students. The participants were 443 Nigerian students enrolled in pre-university science program. Students' self-report on EI and SDL were gathered and analyzed using SPSS 26 and AMOS 24. Exploratory and confirmatory factor analysis were performed to determine cross-cultural validity of the instruments in the Nigerian context. After controlling for gender and age, the hierarchical regression analysis reveals that student academic performance was positively predicted by perceived Interpersonal and Intrapersonal EI, whereas self-directed learning has an inconsistent predictive impact at different steps in the model. Overall, the predictor variables were able to explain substantial proportion of students' academic performance in pre-university program. Insightful suggestions were made.