To resolve the difference between science and religion, various perspectives have been presented; some have tried to put science at the service of religion and have completely rejected scientific findings. On the other hand, another group has abandoned religion by relying on the empirical method. However, there is also a third group that emphasizes the possibility of coexistence and constructive and peaceful interaction between science and religion. Given the difference in perspectives in this field, the purpose of the present study is to examine the theory of religious science from the perspective of Ayatollah Javadi Amoli and analyze its educational implications. The present article, using the combined research method of content analysis and semantics, examines the essence of his theory, which is one of the innovative perspectives in the discussion of religious science, and its educational implications. The research findings show that in his view, the ancient conflict between reason and religion is transformed into a conflict between reason and tradition, and what is truly called science must be religious. The results of the study also illustrate the effects of the aforementioned theory at different levels of the educational system. In addition to the field of educational theorizing for formulating Islamic educational principles and methods, these effects can be analyzed at three levels: educational policy-making, curriculum planning, and the evaluation system.