Malaria has become a major public health problem in Mauritania since the 1990s, with an average of 181,000 cases per year and 2,233,066 persons at risk during 1995–2012. This paper provides the first publicly available overview of malaria incidence and distribution in Mauritania. Information on the burden and malaria species distribution is critical for guiding national efforts in malaria control. As the incidence of malaria changes over time, regular updates of epidemiological data are necessary.