Lots of efforts have been made to make Pakistan a Polio free country for the last two decades, but, Pakistan struggle to be polio free country is not prolific. Pakistan health sector developed vigorous strategies for the eradication of polio in Pakistan, but value of all the strategies is only well documented pieces of paper in plan development due to ineffective implementation. The purpose of the study is identifying the potential factors that are influencing the implementation of polio program in Pakistan. Existing structure, Resistance to Change, Vested Interests and Organizational Culture were taken as independent variables for the effective implementation of the polio program in Pakistan. The regression result shows that there is great influence of the all variables like Existing structure, Resistance to Change, Vested Interests, and Organizational Culture. The result indicated that if the structure of the health sector becomes productive and supportive than the polio may automatically be eradicated from Pakistan.