At the international level, the Institute collaborates with, among others, the World Bank, the International Monetary Fund, UNICEF, Environmental Economics Unit of Gotenborg University (Sweden), Hamburg Institute of International Economics (HWWA), Affiliated Network of Social Accountability (ANSA), and the Institute of Development Studies (IDS) at the University of Sussex.

At the national level, KIPPRA collaborates with, among others, various government ministries, Tegemeo Institute of Agricultural Policy, Institute of Economic Affairs, Institute of Development Studies (University of Nairobi), and School of Economics at the University of Nairobi.

In addition, the Institute collaborates with local public and private institutions in areas of policy formulation, implementation and evaluation. Some of the public institutions include the National Economic and Social Council, Central Bank of Kenya, Kenya Revenue Authority, Retirement Benefits Authority, the Communications Commission of Kenya, the Kenya Tourism Board, local universities, the Nairobi City Council, among others. The private institutions include Kenya Private Sector Alliance (KEPSA), Kenya Association of Manufacturers (KAM) and other umbrella organizations. The private sector is also engaged in conceptualization of research projects and in dissemination. They are also invited during KIPPRA in-house quality seminars and dissemination workshops.