The supreme authority of NESDO Nepal is the Generally Assembly. The Generally Assembly consists of 124 members out of which eight are honorary member fifty four life and sixty two are general member. Every year the members participate in the general assembly. The general assembly of NESDO Nepal mainly aims at providing policy guidance to achieve the intended goals of the organization and approves the annual budget, audit report & next year plan. At the end of every three year the Generally Assembly selects 7 members Governing Board as the executive committee of the Institution.

The Governing Board is the highest policy and decision making body of NESDO Nepal. The Governing Board of NESDO Nepal consists of Seven Members from different professions such as university teachers, Government officials and retired professionals. The Governing Board is responsible for the formulation of plan and budget for various Programs to be implemented by the Organization. The Governing Board evaluates and monitors the implementation of policies, programs. The Executive Director works as Member-Secretary of the Governing Board. The Executive Director is the chief Executive of NESDO Nepal and responsible for the smooth implementation of all activities of the Organization. The Executive Director implements activities through the support staff of the organization.