In 1991 the International Institute for Educational Planning (IIEP) and a number of Ministries of Education in Southern and Eastern Africa began to work together in order to address training and research needs in Education. The focus for this work was on establishing long-term strategies for building the capacity of educational planners to monitor and evaluate the quality of their basic education systems. The first two educational policy research projects undertaken by SACMEQ (widely known as "SACMEQ I" and "SACMEQ II") were designed to provide detailed information that could be used to guide planning decisions aimed at improving the quality of education in primary school systems.
During 1995-1998 seven Ministries of Education participated in the SACMEQ I Project. The SACMEQ II Project commenced in 1998 and the surveys of schools, involving 14 Ministries of Education, took place between 2000 and 2002. The survey was undertaken in schools in Botswana, Kenya, Lesotho, Malawi, Mauritius, Mozambique, Namibia, Seychelles, South Africa, Swaziland, Tanzania, Uganda, Zambia and Zanzibar.
Moving from the SACMEQ I Project (covering around 1100 schools and 20,000 pupils) to the SACMEQ II Project (covering around 2500 schools and 45,000 pupils) resulted in a major increase in the scale and complexity of SACMEQ's research and training programmes.