IAPRI has its roots in the Food Security Research Project (FSRP) which was established in 1999 as a collaborative effort between the Ministry of Agriculture and Livestock (MAL), the Agricultural Consultative Forum (ACF), and Michigan State University (MSU). FSRP began with initial financial support from the United States Agency for International Development (USAID) and, beginning in 2007, from the Swedish International Development Cooperation Agency (SIDA/Zambia). Through this collaborative framework FSRP undertook applied agricultural policy research, capacity building, and outreach activities.

FSRP over the years became a leading institution for empirical agricultural research in Zambia, providing insights on how both government and private firms can raise the productivity of smallholder agriculture, stimulate inclusive economic growth, and improve food security. However, as a donor-funded project FSRP's structure did not provide an obvious exit strategy whereby the research and outreach work that it conducted could be sustainably taken over by a local Zambian institute. To create a sustainable platform for agricultural policy research and outreach in Zambia, MSU transformed the FSRP into IAPRI, Zambia's first locally registered agricultural policy institute.

IAPRI was incorporated in October 2011 under the Companies Act of the Laws of Zambia as a private company limited by guarantee, with a local Board of Directors drawn from various stakeholders including both the public and private sector. The first subscribers to IAPRI include the Ministry of Agriculture and Livestock (MAL), Ministry of Commerce, Trade and Industry (MCTI), Central Statistical Office (CSO), University of Zambia (UNZA), Institute for Economic and Social Research (INESOR), Zambia National Farmers Union (ZNFU), Grain Traders Association of Zambia (GTAZ), Agricultural Consultative Forum (ACF), and two independent esteemed individuals as guarantors. In February 2012 IAPRI was officially launched by the Minister of Agriculture and Livestock, Honourable Emmanuel Chenda.