The management of KIPPRA is vested in a Board of Directors' comprising 13 members (including the Executive Director). Three (3) are Permanent Secretaries (Ministries of Finance; Planning, National Development & Vision 2030; and Trade); two (2) represent special interest groups; seven (7) represent the business sector, universities and research institutes in Kenya; and the Chairman.

The Chairman of the Board is appointed by the President from the non-government members. Board members are appointed by virtue of their integrity, knowledge and experience in matters related to public policy, and understanding of management and social science research procedures. The Board operates through four committees: Finance; Audit; Programmes and General Purposes.

The Executive Director
The Executive Director, who is the Secretary to the Board, reports to the Board of Directors. The Board appoints the Director through a competitive process. The Director is responsible for directing the affairs and transactions of the Institute, and ensures the preparation and implementation of the work programme.

Divisions
The Institute has five research divisions: Macroeconomics, Productive Sector, Social Sector, Infrastructure and Economic Services, and Private Sector Development. The research divisions are supported by KIPPRA Information and Documentation Centre (KIPDOC), a modern documentation centre which provides access to various government publications, and national and international datasets, among others.

Further, the research divisions are supported through a modern Information Technology and Communication infrastructure. The Institute has also established specialized computer laboratories for training, and for macroeconomic modelling. The IT section also supports research activities in terms of data management and analysis by availing/implementing the required tools such as databases and statistical software. The section also supports the Institute by availing archived data.

The Finance and Administration Division supports the entire Institute in terms of providing finance and accounting services, and general administration. The division also closely monitors project implementation through state of the art project management modules in the finance and accounting software.

The Heads of Divisions assist the Executive Director in implementing the activities of the Institute.