Mozambique, along with South Africa, is one of the three priority countries for Flemish development cooperation. The cooperation started in 2002. In the initial period from 2002 to 2006, collaboration was mainly project-oriented and on a relatively small scale. The focus was solely on the fight against HIV/Aids. As of 2006, the cooperation has been more structured. Health care was supported sector-wide, in addition to projects in the education sector, and this was then implemented specifically in cooperation with the province of Tete. 

From 2011, the focus was exclusively on health. In consultation with the Mozambican Government, a new country strategy took effect in 2016, supported by a radical innovation: a consistent focus on adolescents (10 to 19-year-olds) as one of the most vulnerable groups in Mozambican society in terms of health. The focus on health and the Tete province is still in place.

As of 2021, the fourth Country Strategy Paper came into place. The focus on health care continues. Further efforts are being made to develop a stronger and more efficient health system. Flanders also continues to focus on improving access to sexual and reproductive health care. The previous focus on mainly female adolescents is extended to additional vulnerable groups.