Although the U.S. government has made significant efforts to achieve gender equality, there still are some gender-based differences in worker compensation. This study investigates the existence of salary disparity by sex, academic rank, pre/during-COVID pandemic, and size of universities within Science, Technology, Engineering, and Mathematics (STEM) programs. We base our empirical analysis on data gathered from the faculty of 4-year public universities in one state in the south-central U.S. in 2018 and 2021. We use factorial N-way ANOVA to control for faculty heterogeneity. Our analysis showed size, rank, year, and sex are all significant factors. Smaller universities pay less than larger public universities, the more senior tenured ranks make more, and pay did increase from 2018 to 2021. There are interesting findings when considering sex, as men earned more than women in STEM in both 2018 and 2021 as well as at all three school sizes. The exception was for full professors. Our study provides fresh insights into the gender pay gap, especially in male-dominated academic disciplines.