The trend of escalation religious intolerance in many countries to be a potential trigger proliferation of disputes and conflicts, in which it will have an impact on security and stability threats, deterioration of economic aspects, social-cultural and even may affect on the destruction of civilization of a country. Indonesia, the country with the largest degree of heterogeneity in the world that has diverse ethnicities, cultures, customs, language, religions, must continue to build and develop an attitude of tolerance, particularly religious tolerance. Islamic Boarding School as an Islamic educational institution, a place of propaganda and dissemination of religious teachings of Islam, are expected to to build and develop an attitude of religious tolerance to their students more optimally. An enhancement of religious tolerance attitude of students conducted through a learning management by implementing a variety of learning theory and comprehensively via methods of sorogan, bandongan, fathul kutub, muhawarah, mudzakaroh and memorization which is based on ukhrawi. While the effectiveness of classroom management carried out by making the students as learning subjects so it motivate students in the development of their cognitive, affective and psychomotor. Pupils that have a tolerance are expected to uphold the attitude of respect, appreciate, recognize and simplify to preaching in public.