Malaria transmission is influenced by climate, land use and deliberate intervention. The study provides quantitative data comprising 50,424 surveys at 36,966 geocoded locations to cover 115 years (1900 – 2015) of malaria history in sub-Saharan Africa. The results show that the African continent has witnessed a long-term decline in the prevalence of Plasmodium falciparum from 40% prevalence in the period 1900–1929 to 24% prevalence in the period 2010–2015, a trend that has been interrupted by periods of rapidly increasing or decreasing transmission. The cycles and trends of plasmodium falciparum prevalence from 1900 to 2015 are inconsistent with simplistic explanations in terms of climate or intervention alone. The study highlights that focus on one factor alone is too simplistic and does not adequately explain the cycles of parasite prevalence.