Religious intolerance is spreading within the Indonesian institution of education. Previous studies have shown that the growth of intolerance is due to the state’s regulation and pedagogical apparatus. In contrast to the previous studies, I argue that the intolerance is related to hidden curriculum applied by the institution of education.  Normatively, the hidden curriculum contains the value of religious tolerance. However, factually, the author found that there are practices of intolerance, through the formal and informal spheres in the school’s structure, within the hidden curriculum. This article applies a qualitative approach with a mixed method research strategy to analyze data collected from students, teachers, and alumnis through field observation, in-depth interview, and survey.