The construction of the metaphysics of divinity that exists in the Islamic higher education system, especially in Perguruan Tinggi Keagamaan Islam Negeri (PTKIN) - in the form of universities) in Indonesia has been finalized and established. It turns out that there was a logic of metaphysics of divinity that was different from the mainstreaming of the established metaphysics, namely metaphysics (apophatic theology). Based on this reality, this study focused on the construction on the concept of apophatic theology that grew and developed in the Islamic higher education system in PTKIN (namely UIN Sumatera Utara, UIN Malang, and UIN Jember). The research problem in this study was how does the construction of apophatic theology in the Islamic higher education system develop at UIN Sumatera utara, UIN Malang, and UIN Jember? In order to analytically answer this question, this study used a qualitative approach with data collection techniques; such as in-depth interviews, participatory observation, and documentation. The data analysis used interactive data analysis from Miles, Hubermann, and Saldana. This study found that apophatic theology was positioned as a discourse of profetization of divine values expressed through a negative style. The theological construction basically "rejects" divine knowledge with the logic of negation and paradox. This apophatic theology in the Islamic higher education system builds an axiological framework that more oriented towards the dimensions of humanity and divinity; or the profane dimension and transcendental.