Institutional imbalance has been the hall mark in the state of Pakistan right from the time of its inception in 1947. It has inherited the whole state apparatus from the British Raaj, including legal, political and military institutions. Talking about administrative and political institutions, especially the military one, remained imbalanced in terms of their respective maturity and growth. Main reason for the institution imbalance is our weak political institution and non-democratic political parties which could not bring strong dynamic and sustainable political institutions. Failure of political administration and bureaucratic regimes caused to create space for army into the political domain which was more organized, strong and disciplined. During the history of Pakistan four military regimes have imposed martial law, political activities and parties were banned, censorship on media was imposed, assemblies were dissolved and constitution was suspended and abrogated. Besides the mentioned internal factors, external factors like geo-strategic location of Pakistan and its security-centered foreign policy also plays important role in supporting such anti-democratic steps by the military. The findings revealed that poor governance and legitimacy crises has contributed to the imbalance between the civil-military relations. This study investigated to discern the fluctuation in the Civil-Military relations, especially during Musharraf regime. Qualitative and Quantitative methods have been used to analyze the variable dynamics which interplay significant role in the Civil-Military relations.