The epidemiological surveillance of malaria is a necessary intervention for eliminating the disease from the planet. The international border zones of the Amazon continue to be highly vulnerable to malaria since population mobility impedes elimination. Although in the past few years, cases of malaria have had an essential reduction in Brazil, this trend was not confirmed in municipalities along the border. This study aimed to establish the epidemiology of the disease during the last 13 years in Oiapoque, a Brazilian municipality at the international border with French Guiana, an overseas department, to develop strategies for the control/elimination of malaria in these areas.