The various perspectives on religious science indicate a variety of intellectual approaches in this field. Ayatollah Javadi Amoli’s theory of religious science, one of the prominent theories on this science, has garnered significant attention among scholars. Institutionalizing this theory could lead to a substantial transformation all over the world. This study examines the challenges and functions of his theory on religious science. The findings reveal challenges such as the confrontation with atheistic science, the conflict between intellect and revelation, the institutionalization of nature instead of creation, the potential conflict between the results and products of empirical knowledge and religious science, the establishment of identity-erasing Western science, the challenge of the confrontation between revelation and intellect, and the presence of Qarun-like thinking among scientists as the main obstacles to the realization of religious science. These challenges require independent research; however, this study merely explains the challenges and provides a brief response to them. Additionally, the functions of this theory include a maximalist approach to religion, the unity of science and religion, the comprehensiveness of epistemic sources, human perfection, attainment of pure life, the unity of Islamic seminary (Hawza) and university, the synergy of reason and revelation, acceleration in civilization-building, access to a source beyond reason, and resolving the conflict between science and religion. These functions pave the way for transformation in Islamic civilization and provide a platform for interaction among various fields of knowledge. This study emphasizes the importance of this theory as a solution to contemporary challenges and the utilization of upcoming opportunities.