Objectives: To assess the correlation between the burden of seven priority neglected tropical diseases (NTDs) included in the Brazilian National Agenda of Priorities in Health Research - tuberculosis, Chagas disease, leprosy, malaria, leishmaniasis, dengue and schistosomiasis - and their respective research funding and output. Methods: This retrospective review obtained data on disease burden from the Global Burden of Disease Study and funding data from open access sources. Publications were retrieved from Scopus and SciELO, and characterised according to the type of research conducted. Correlation between funding, research output and burden was assessed by comparing the 'expected' and 'observed' values for funding and publications relative to the proportional burden for each disease. Results: There was an emphasis in basic biomedical research (average 30% of publications) and a shortage of health policy and systems (average 7%) and social sciences research (average 3%). Research output and funding were poorly correlated with disease burden. Tuberculosis, Chagas disease and schistosomiasis accounted for more than 75% of total NTD-related DALYs, but accounted for only 34% of publications. Leprosy, leishmaniasis and malaria, together, received 49% of NTD-related funding despite being responsible for only 9% of DALYs. Conclusions: The analysis evidenced a lack of correlation between disease burden, research output and government funding for priority NTDs in Brazil. Our findings highlight the importance of monitoring health needs, research investments and outputs to inform policy and optimise the uptake of evidence for action, particularly in developing countries, where resources are scarce and the research capacity is limited. The results contribute to health policy by highlighting the need for improving coordination of scientific activities and public health needs for effective impact.