Civil Military Relation in Nepal faced a new challenge in post conflict setting especially when the rebel force became the largest political party in Constitution Assembly election and Ministry of Defense; the higher command of the national army came under the direct control of its so called former enemy of the national army. The debate over integration of former rebel combatants in the Nepalese Army remained at heart of the peace process. Amid this situation, through structured focused comparative case studies of El Salvador and Mozambique, this paper draws lesson to improve CMR in Nepal in terms of civilian control and military professionalism. It uses the lens of traditional literature on Civil Military Relation to compare and analyze the military reform in peace agreement and its implementation process.