One of the main challenges faced by companies, scholars, and governments nowadays is achieving economic, environmental, and social sustainability. Remote working, reduced work weeks, and other types of flexible working time arrangements (FWAs) are the new characteristics that will shape the future of work to ensure social sustainability. In changing work patterns, working styles are changed to possibly improve women employees’ mental health and life–work balance. However, recently, very few firms have succeeded in adopting these new FWA trends. The purpose of this paper is to investigate women’s preferences towards FWAs in the academic sector as a social sustainability source. We investigate the effect of the COVID-19 pandemic on female faculty members’ future job preferences. The data used in the research are collected from a survey given to female faculty members who work in a Saudi women’s university and have already experienced FWAs during the COVID-19 period. The study uses mixed methods of research, combining a choice modeling (CM) method, one sample t-test, a paired sample t-test, cluster analysis, and probit models. Our results show that flexible working arrangements improve the wellbeing of women employees, which ensures sustainable social development. The findings also show that flexibility in location plays a significant role in the decision made by female faculty members when revealing their flexibility preferences. However, flexibility in time did not play a significant role in the decisions made by respondents. This study adds to the empirical evidence in the current literature on female academic staff preferences for FWAs in Saudi Arabia, using choice modeling conjoint analysis and mixed approaches.