Neighbourhood-level data on monthly wMel prevalence in Aedes aegypti and dengue notified cases, underlying the analyses and figures in the submitted manuscript 'Effectiveness of Wolbachia-infected mosquito deployments in reducing the incidence of dengue and chikungunya in Niteroi, Brazil: a quasi-experimental study'. The neighbourhood-level analysis (and dataset) now excludes Jurujuba neighbourhood in Zone 1 where pilot releases were conducted in 2015-16, because the wMel monitoring in 2015-16 in Jurujuba was only representative of the small release areas whereas the case data is for the whole neighbourhood.