The purpose of this study was to look into the factors affecting the academic performance of Pre-Service Science Teachers of a state university, specifically, West Visayas State University. The data of this descriptive research were gathered using the checklist instrument administered to 283 Pre-Service Science Teachers, which comprise the entire population of BSED (Biology, Physics and Physical Science) students of the West Visayas State University, school year 2015-2016. The descriptive statistical tools employed were the mean, standard deviation, and ranking while the inferential statistical tools employed were the t-test for independent samples and One-Way Analysis of Variance (ANOVA). The respondents were classified according to sex, family income or socio-economic status (SES), and year level. The findings revealed that the main factors that affected the most in the academic performance of Pre-Service Science Teachers were personal-related such as laziness, health condition, and lack of focus. On the other hand, social-related factors had the least effect on Pre-Service Science Teachers’ academic performance. Specifically, they were least affected by competition among relatives/neighbours as this was not very rampant among Pre-Service Science Teachers in state universities. Male Pre-Service Science Teachers were more affected by school-related factors than the females. The first year Pre-Service Science Teachers were more affected by the personal factors, school-related factors, and social factors than the second year and third year Pre-Service Science Teachers. Moreover, Pre-Service Science Teachers with low SES were significantly affected by family and home-related factors than Pre-Service Science Teachers with high SES.