Plasmodium vivax remains a public health problem in native communities from Condorcanqui, living on the banks of the Santiago River in the Amazonas Region of Peru. In this study, we analyzed the P. vivax malaria database reported by the Regional Directorate of Health-Amazonas (DIRESA) between 2005 and 2020, in order to describe the situation of malaria in this region, and determine significant changes in malaria vivax incidence through time in relation to changes on malaria control policies. A total of 6,974 P. vivax cases were reported in over one hundred native communities. Cumulative incidence per 1000 habitants (CI) was estimated with a 95% CI and Chi-square was used to evaluate changes in the distribution of malaria cases according to gender or age through time. Our results showed that there was a significant decrease of cases from 2006 (CI: 23.5) to 2013 (CI: 0.018) which could be explained by an active malaria control program and a Global Fund-supported intervention (PAMAFRO, 2005–2010). However, when those programs ended, cases continue to increase up to CI: 26,6 in 2020. On the other hand, there was not a significant change in the distribution of malaria cases by sex; however, there was a significant difference in the distribution of malaria cases by age. Most of the cases corresponded to children under eleven years of age (49,8%), which represents the most vulnerable group. Although further studies are needed, changes on malaria cases through time revealed the need for a sustained malaria control program that could lead for malaria elimination in this low transmission setting.