WAVE Foundation has two-tiered governance system as per the organizational policy. Policies are formulated through the participation and approval of General Body consisting of eighteen (18) members and Governing Body of seven (07) Members. Governing Body reserves the highest authority in regard to policy formulation and approval as per the organizational policy. Members of Governing Body are elected for two years. Governing Body meetings are conducted at least six times a year.

Executive Director is entrusted with the responsibility of proper management and persecution of policies and planning of the Organization. He acts as the Chief Executive of the organization and serves as the General Secretary of the Governing Body.

Management of the organization could be divided into two tiers as Senior Management Team (SMT) and Central Coordination Team (CCT).

SMT plays vital roles in decision-making, policy-review, evaluation, corrections and making new policy proposals. Apart from that SMT explores new horizons for explorations and works as bridge between the Organizations and donors. All officials functional in the directorial posts along with the Executive Director are the members of SMT. Executive Director coordinates the Senior Management Team.