HAPEN management structure is designed to encourage flexibility and autonomy on the part of its 20-core management and support staff. The structure creates space for intellectual creativity and innovation and encourages staff members and other partners to be productive in desirable working conditions. It is also designed to ensure maximum accountability. The key management organs of HAPEN comprise the Board of Directors, Executive Director, Programme Coordinators, Admin/Finance and support staff. For the smooth day to day operations as well as effective and efficient administration of interventions, HAPEN has developed functional management practices, stringent internal control systems and policies to guide key management aspects.

The most important of these include the Memorandum and Articles of Association, Financial Policy, Procurement Policy, Human Resource Development Policy, and Project Implementation Policy, External Relations and Services policy, management Practice policy and Governance