Gendered organizational conditions create the context for persisting differences between men and women in the workplace. Within, higher education, this manifests as a salary gap between male and female faculty members. The academic capitalistic policy environment creates the conditions for increasing competition for external funding, especially in the areas of research and science and engineering. The change in the academic climate may sustain or intensify the gendering of universities as organizations. Universities with the highest level of research activity were chosen for this study and formed the 130 public institution sample. This study used fixed effects panel regression analysis to explore the relationship between the faculty gender salary gap and institutional emphasis on research as well as science and engineering. In addition, the relationship between institutional emphasis and the faculty gender salary gap was explored over time with the inclusion of a time trend and temporal interaction terms. Results showed that the higher the percentage of female faculty members, the greater the faculty gender salary gap for assistant professors. In addition, science and engineering emphasis over time had a significant impact on the professor salary gap with a decreasing effect both at the mean and one standard deviation above the mean, but with an increasing effect on the salary gap for institutions one standard deviation below the mean. When taking action to increase gender equity, it is important for universities to recognize that the faculty gender salary gap occurs in an organizational context impacted by institutional-level conditions.