Background: Malaria causes 400 thousand deaths worldwide annually. In 2018, 25% (187,693) of the total malaria cases in the Americas were in Brazil, with nearly all (99%) Brazilian cases in the Amazon region. The Bolsa Família Programme (BFP) is a conditional cash transfer (CCT) programme launched in 2003 to reduce poverty and has led to improvements in health outcomes. CCT programmes may reduce the burden of malaria by alleviating poverty and by promoting access to healthcare, however this relationship is underexplored. This study investigated the association between BFP coverage and malaria incidence in Brazil. Methods: A longitudinal panel study was conducted of 807 municipalities in the Brazilian Amazon between 2004 and 2015. Negative binomial regression models adjusted for demographic and socioeconomic covariates and time trends were employed with fixed effects specifications. Results: A one percentage point increase in municipal BFP coverage was associated with a 0.3% decrease in the incidence of malaria (RR = 0.997; 95% CI = 0.994–0.998). The average municipal BFP coverage increased 24 percentage points over the period 2004–2015 corresponding to be a reduction of 7.2% in the malaria incidence. Conclusions: Higher coverage of the BFP was associated with a reduction in the incidence of malaria. CCT programmes should be encouraged in endemic regions for malaria in order to mitigate the impact of disease and poverty itself in these settings.