As a new concept, the definition of human security has been widely contested. It relates to the issues of human security ‘for whom’, ‘from what’ and by ‘what means’. Dealing with the first issue, scholars generally agree that the focus of it is protecting the individual rather than the state's security. But, dealing with two other central issues, scholars seem to hardly agree upon. This paper deals more with the third question focusing on pesantren (a traditional Islamic boarding school) that largely exists in Indonesia. One of the reasons is, as having religious-based local wisdoms, the pesantren has long time concerned with human security without necessarily trapped by either ‘for whom’ and ‘from what’ debates. The second reason refers to its social mission of securing people which seems to be valuable in balancing the continuing hegemonic discourse of putting the state as the ultimate reference of security. The last is related to the contemporary challenge for human security. As Acharya indicates, currently, securitization of religion is politically sensitive due to the fact that it closely related to or even being the basis of the new global politics identity. In this sense, I argue that the role of religious-based institution, particularly the pesantren, should not necessarily be seen as something incompatible with human security. Having its good practices, it may even suggest a new perspective of understanding human security by making use of religious-based local wisdom concept. This research used qualitative methodology supported by ethnography approach. Though some data from secondary sources were present, most supporting data were collected through various interviews to digging up first-hand perspectives.