Indonesia as a multicultural country has a very complex diversity. More differences create greater potential for disunity as well as conflicts between ethnic and cultural groups. Inculcating values of tolerance towards students in Indonesia is a must, because Indonesia does not only consist of one understanding, religion, ethnicity and culture. Therefore, a uniter for Indonesians in order to make the nation live in harmony is needed. One of the concerns is regarding to the religious tolerance in Indonesia. This qualitative research was conducted in Cilacap at Immaculata Foundation, by using observation, interview, and documentation techniques. The data analysis used was interactive analysis, including data reduction, data display, and data conclusion. The findings of this study describe that the values of religious tolerance are applied through routine activities, such as respect, mutual help, cooperation, equality, freedom, justice, and responsibility which are internalized through exemplary, habituation, and the giving of advice to keep the harmony among religions.