Established in 2000-2001, the Center for Religious and Cross-cultural Studies (CRCS) is the only master's level religious studies program at a non-religiously affiliated university in Indonesia. In many respects, the program is experimental, operating within the dynamic political and religious environment of the Muslim world's youngest and largest democracy. Like other large democracies such as India or the United States, the Indonesian government and courts have their challenges and opportunities in navigating a multiplicity of religions. In Indonesia, this took on particular urgency in the context of religiously-charged conflict in the 1990's and early 2000's which helped lead to the establishment of the CRCS. This paper seeks to explore how students and key faculty relate to the program's mission and approach to the study of religion while tracing the development of religious studies as a discipline in Indonesia. Special attention is paid to the political and, at times, controversial aspects of approaching religion with secular and pluralistic frameworks and language. It was informed by interviews and surveys conducted between January and May of 2010.