Padakhep stresses high priority in transparency and accountability in administration and accounts that ensure good governance of the organization. Padakhep has three-tier organizational structure, namely: 1) General Body, 2) Executive Committee and 3) General Administration. The General Body comprises a group of highly distinguished professionals of the society. It consists of 21 members and holds at least one general meeting annually. The General Body approves all the activities of the Executive Committee.
The Executive Committee (EC) elected by the members of the General Body for 5 years, consists of 7 members who bring their diverse skills and experience to the governance of Padakhep. It is the supreme authority to frame policies and guidelines to run the organization. It consists of President (1), members (5) and Member-Secretary (1). The EC holds at least 3 meetings (every 4 months) a year. The EC has been continuously guiding the organization not only to face the current challenges but also to prepare it to play its due role in upholding its image as one of the leading NGOs. The Executive Director, appointed by the Executive Committee, plays the role of member-secretary of the EC in accordance with the recognized rights and responsibilities of the designation. The Executive Director, the administrative head of the organization, is responsible for overall administration and implementation of its different development programs/projects and related activities.