Malaria is endemic in Madagascar and a leading cause of mortality and morbidity. Its geographical distribution is heterogeneous throughout the country, in relation to climatic, environmental and social factors. In this study, we analyze the spatiotemporal distribution of malaria caused by Plasmodium falciparum. The Service for Health and Demographic Statistics of the Ministry of Public Health provided monthly epidemiological data related to complicated and uncomplicated malaria cases from 2010 to 2014. We analyzed and integrated these data into a Geographic Information System to map malaria trends by year, by month and by age for each district. The incidence of malaria has increased since 2012 and remains high in some coastal districts. The highest peaks of reported cases are observed between January and April with especially high incidences along the Eastern coast. The average of uncomplicated malaria cases of children less than five years represent about 36% of cases for each year. Both complicated and uncomplicated malaria show similar patterns and trends. The quality of epidemiological data is discussed regarding the provision and access to health services. The connectivity between districts and the persistence of malaria on the coast could induce the emergence of malaria in central highlands following reintroduction by travelers. Thus, non-endemic areas are at risk of emergence with complicated clinical malaria form. Districts presenting significantly high incidences should be carefully monitored in order to reduce transmission.