Academic performance in primary students is fundamental to future school success; however, simultaneous analysis of different key individual, family, and teaching factors must be considered to improve understanding and benefit the development of students’ potential. This article presents a latent regression analysis model that examines the relationship between the latent variables (self-efficacy, interest in reading, bullying, parental expectations, and discrimination/exclusion, and teacher violence/aggression) and the academic performance of first-cycle primary students. The model investigates the impact of the latent variables on the standardized endogenous variables of SIMCE Mathematics and Language test scores using a quantitative, non-experimental, correlational, and cross-sectional design. The study involved 70,778 students (53.4% female), with an average age of 9.5 years (SD = 0.6), from Chilean public (33.6%) and subsidized (66.4%) schools. The results indicate that the model accounted for 49.8% and 47.7% of the mean variability in SIMCE Mathematics and Language test scores, respectively. The goodness-of-fit indices demonstrated satisfactory fits for both models. In both tests, student self-efficacy emerged as the most significant factor explaining test score variability, followed by parental expectations. Bullying was identified as a relevant factor in reducing mean performance on both tests. The findings suggest that education decision makers should address these issues to improve student outcomes.