Understanding local epidemiology is essential to reduce the burden of malaria in complex contexts, such as Brazilian municipalities that share borders with endemic countries. A descriptive study of malaria in the period 2003 to 2020 was conducted using data from the Malaria Epidemiological Surveillance Information System related to a remote municipality with an extensive border with Peru to understand the disease transmission, focusing on the obstacles to its elimination. The transmission increases at the end of the rainy season. During the period of 18 years, 53,575 malaria cases were reported (Mean of API 224.7 cases/1,000), of which 11% were imported from Peru. Thirteen outbreaks of malaria were observed during the studied period, the last one in 2018. The highest burden of cases was caused by P. vivax (73.2%), but P. falciparum was also prevalent at the beginning of the study period (50% in 2006). Several changes in the epidemiological risk were observed: (1) the proportion of international imported cases of malaria changed from 30.7% in 2003 to 3.5% in 2020 (p<0.05); (2) indigenous people affected increased from 24.3% in 2003 to 89.5% in 2020 (p<0.0001); (3) infected children and adolescents < 15 years old increased from 50.2% in 2003 to 67.4% in 2020 (p<0.01); (4) the proportion of men decreased from 56.7% in 2003 to 50.4% in 2020 (p<0.01); (5) the likelihood of P. falciparum malaria has significantly declined (p<0.01). The number of cases and the incidence of malaria in 2019 and 2020 were the lowest in the period of 18 years. The burden of malaria in indigenous areas and its determinants, seasonality, geographical access and the long international border are obstacles for the elimination of malaria that must be overcome.