It is difficult to find a compromise in an ethnic minority conflict, especially those involving in religious question. In general, ethnic minority conflict isolates the affected area, which caused to hamper social and economic development and to nest various criminal elements such as drug and trafficking. Such situation creates a negative image of the very ethnic minority among the majority populace, and continues by the people who takes advantage of the unstable situation. The existing theories on ethnic minority conflict did not place the human right issue of the ordinary people in the conflict zone so that the theories could not provide a genuine solution for the conflict. Complementing the existing theories, this paper presents three variables to accomplish the peaceful solution for ethnic minority conflict - existence of neutral third party mediators, strong political leadership based on the popular consensus, and the future oriented reform programs. As a result of examining the past and present efforts to solve the Philippine Muslim minority conflict, the present Aquino government`s ‘Comprehensive Agreement on the Bangsamoro’ have more positive aspects in a comparative perspective. However, due to the weakness in the political leadership which bringing up the popular consensus on the issue, the present peace agreement with the MILF could not assure the desired solution to the four decade long conflict.