Leadership is a very important thing in an institution. Pesantren is an educational institution that makes the Kiai the center in almost everything. This research raises a research problem, how is Kiai's leadership in the transformation of pesantren’s institutional and educational systems based on the perspective of transcendental structuralism? Consequently, this research used a qualitative approach of a phenomenology type and multi-site design. Data collection was conducted through in-depth interview techniques, participant observation, and documentation; while the data analysis used was an interactive analysis of the Miles et al. (2018). The results found that Kiai leadership as a structure in the pesantren was able to initiate the emergence of pesantren transformation, namely from an educational institution based on and oriented to theocentric to becoming the anthropocentric one. Therefore, the developing values of institutional management in pesantren have appeared based on the combination of human and divine values (divinity and humanity). It is the basis that has encouraged Kiai leadership to produce a kind of pesantren management from a belief entity or fidelity (faith) guided by the acumen of rational-empirical knowledge (science) and operationalized in the form of pesantren’s institutional management. The researchers believe that, in this context, anthropocentric leadership can develop institutional management and integrative education systems.