This study aims to analyze the strategic role of the Senate in the selection of leadership at UIN Sunan Kalijaga. This research critiques the reduction of the Senate’s authority due to recent regulatory changes and examines how these changes affect leadership selection and governance in higher education institutions. This research employs a mixed-method approach, combining qualitative document analysis and quantitative survey methods. Key documents such as Minister of Religious Affairs Regulation No. 68/2015 and related decrees were analyzed. Additionally, a survey was distributed to Senate members to assess their perceptions of the regulatory changes and their effects on the leadership selection process. The findings reveal that the reduced authority of the Senate significantly impacts the transparency and accountability of the leadership election process. Senate members express concerns that external political influences and bureaucratic involvement have undermined the meritocratic values that traditionally guided leadership selection. The study is limited to a case study of UIN Sunan Kalijaga, which may not fully represent other Islamic universities. Future research should explore the effects of similar regulatory changes in different institutional contexts to enhance generalizability. This research provides a critical perspective on the effects of governmental intervention in academic governance, particularly in leadership elections at Islamic higher education institutions. It highlights the tension between maintaining academic autonomy and the influence of external regulations.