Abstract Background Brazil has considerably reduced the number of cases of malaria in recent years and aims to eradicate the disease completely, however, vivax malaria continues to be a major challenge for the health system. In this context, the key to building a successful elimination programme may lie in the knowledge and the perceptions of the health agents, the patients affected by the disease and the personnel responsible for malaria diagnosis, treatment and control at the local level. Methods A qualitative study was undertaken in Manaus, capital of the state of Amazonas, Western Brazilian Amazon, using a sample of 33 patients who were being treated for malaria and 22 health agents who were working in malaria diagnosis, treatment and control at the local level. A semi-structured interview with a further thematic analysis was performed. Results There are still many myths regarding malaria transmission and treatment that may hinder the sensitization of the population of this region in relation to the use of current control tools and elimination strategies, such as mass drug administration (MDA). Most health professionals reported that the abandonment of treatment for malaria by the patient is related to poor social conditions, the high incidence of alcoholism and the low level of schooling of the affected population. One negative perception, observed in both groups with regard to the use of insecticide-treated nets, is that they may cause skin irritations and allergies. Most patients and health professionals have described malaria as an impossible disease to eliminate because it is intrinsically associated with forest landscapes, and according to them, elimination would only be possible if there were a vaccine against malaria. Conclusion In the Amazon, cultural perceptions about the etiology of this disease can influence the behaviour and practices that social groups adopt in relation to the different forms of living in a malaria-endemic context. Negative perceptions about malaria elimination can act as a barrier when trying to reach proper coverage for control strategies such as mosquito nets and MDA.