We present this study as a contribution to celebrate “the International Day of Women and Girls in Science”. Women’s empowerment in scientific research is a crucial issue in the United Nations “2030 Agenda for Sustainable Development”. This study aimed to investigate the obstacles facing women researchers in scientific research in Saudi Arabia. A cross-sectional survey was used to assess women researchers’ perceptions towards the roles of universities, donors and women researchers. Descriptive statistics, correlation and regression analysis were used for data analysis. Findings showed that the overall assessment of women’s empowerment in scientific research is moderate and faces a mixture of obstacles mainly due to dissatisfaction with the role of donors. Moreover, the role of universities has not yet reached a satisfactory level, while the role of women researchers was satisfactory. The results demonstrated that the role of the university enhances the role of the donor institutions, while the role of researchers has a significant positive influence on the role of the university. No significant association between the role of the researchers and donors was achieved. In conclusion, despite the great achievement by women researchers in empowering themselves as scientific researchers, they still need more support from the university and donors.