The NPRC is structured as follows:

1. NPRC Members (Commissioners): Under the leadership of the Chair, the Commission is the apex policy body. It oversees the operations of the Commission in accordance with the Act and drawing mandate from the Constitution.
2. NPRC Staff (Secretariat):  Under the leadership of the Executive Secretary, the Secretariat is mandated to lead the development of annual work plans for effective implementation of the strategy. The Secretariat is the operational arm of the Commission.
3. NPRC External Committees: Four external committees   – Victim Support, Gender and Diversity; Prevention and Non-Recurrence; Healing and Reconciliation; and Research and Knowledge Management  serve as multi-stakeholder platforms for the Commission providing advisory support to the NPRC in accordance to the Act and Regulations.
4. NPRC Internal Committees: Three internal committees  –  Complaints Handling and Investigations; Resource Mobilisation and Partnerships; and Finance, Human Resources and Administration Committee play a supportive role to the Secretariat on issues of complaints handling, finance and administration and resource mobilisation.