SAAPE functions as a regional alliance of civil society networks facilitating linkages among and between groups in the region, throughout the global South and with the groups in the North. The structure of SAAPE is comprised of the General Assembly (GA),Annual General Meetings (AGM), Advisory Committee, Core Committee, Campaign Focal Organisations and the Regional Secretariat. The GA is composed of all the members who meet in every three years to give policy directions to the entire SAAPE movement. It is the highest policy making body of SAAPE. The AGM is comprised of campaign focal organisations, advisory committee members, core committee members, regional co-ordinator, the secretariat staffs and selected representatives representing different campaign groups from the region. The AGM reviews annual programme and planning of the SAAPE initiatives, both at programmatic as well as administrative levels. It meets every year. 

The core committee members and advisory committee members provide political leadership to the SAAPE movement. The members of core committee come from the campaign leading organisations, country groups, European partner organisations and the Regional Secretariat. The core committee meets twice in a year to review and redesign political intervention strategies at the regional and international levels. The advisory committee of SAAPE provide requested advices to the core committee, and generally meet along with the core committee meetings.

The campaign focal organisations are the campaign leaders that are responsible for planning, implementation, monitoring and evaluation of the campaign activities falling under their respective campaign. Based on the regional nature of the SAAPE campaigns and movements, each of the campaign is coordinated by an organisation at the regional level whereas the activities at the country level are coordinated by respective country groups. Currently, there are three campaign groups, each having its Country Focal Organisation in each country. The country focal organisations are supported by other members of the group to operationalise the SAAPE initiatives in their respective countries. The campaign groups administer campaign activities under their theme in a coordinated way. Whereas, there is also a strong collaboration and coordination across the campaign activities at all levels of their operation. 

To facilitate administration of the SAAPE initiatives, a Regional Secretariat supported by Regional Co-ordinator and some Secretariat staff is established. At present, the Regional Secretariat is hosted by the Rural Reconstruction Nepal (RRN) in Kathmandu, Nepal. The Secretariat facilitates, coordinates and expedites the regional as well as country initiatives from the regional perspective; provides support to the country initiatives and campaign groups as and when necessary; disseminates information at the international level; and liaises with different stakeholders. To facilitate implementation of the campaign activities and coordination between the campaign groups and the Regional Secretariat, a focal person is stationed at each leading campaign organisation to work as an extended arm of the Regional Secretariat.