The National Library of Medicine (NLM) and the Fogarty International Center (FIC) conceived the idea of fostering a health and medical journal capacity-building program in Africa out of concern for the limited production, distribution, and availability of African health information. African health and medical journals are poorly represented in international indexing services, and with such poor representation health and medical research reported in African journals is not readily available even to African care providers.

What came to be known as the African Journal Partnership Program began with a meeting hosted by the British Medical Journal in London in September 2003 for African journal editors to identify their needs. NLM selected the editors and journals from countries that had active NIH-sponsored research and were part of the communication network developed by NLM for its Multilateral Initiative on Malaria.

An initial contract was awarded in May 2004 and four African journals were partnered as follows:

African Health Sciences with the BMJ
Ghana Medical Journal with The Lancet
Malawi Medical Journal with JAMA
Mali Medical with Environmental Health Perspectives and the American Journal of Public Health

A second contract was awarded for a five-year period in July 2008. During that time, the Ethiopian Journal of Health Sciences, Annales Africaines de Médecine, Sierra Leone Journal of Biomedical Research, Annals of Internal Medicine, and the New England Journal of Medicine joined the program, and multiple partnerships, including some within Africa, were established.

A third contract was awarded in 2013 and in 2016, Annals of African Surgery and Rwanda Journal, Series F: Medicine and Health Sciences were welcomed to the program.

The AJPP conducts regular evaluations to monitor achievement of program objectives by each journal and is considering the addition of additional African journals.