BackgroundUse of insecticide-treated net (ITN) has been identified by the World Health Organization as an effective approach for malaria prevention. The government of Uganda has instituted measures to enhance ITN supply over the past decade, however, the country ranks third towards the global malaria burden. As a result, this study investigated how individual, community and region level factors affect ITN use among women of reproductive age in Uganda.MethodsThe 2018–2019 Malaria Indicator Survey of Uganda involving 7798 women aged 15–49 was utilized. The descriptive summaries of ITN use were analysed by individual, community and region level factors. Based on the hierarchical nature of the data, four distinct binomial multilevel logistic regression models were fitted using the MLwiN 3.05 module in Stata. The parameters were estimated using the Markov Chain Monte Carlo (MCMC) estimation procedure and Bayesian Deviance Information Criterion was used to identify the model with a better fit.ResultsThe proportion of women who use ITN was 78.2% (n = 6097). Poor household wealth status [aOR = 1.66, Crl = 1.55–1.80], knowing that sleeping under ITN prevents malaria [aOR = 1.11, Crl = 1.05–1.24] and that destroying mosquito breeding sites can prevent malaria [aOR = 1.85, Crl = 1.75–1.98] were associated with higher odds of ITN use. ITN use attributable to regional and community level random effects was 39.1% and 45.2%, respectively.ConclusionThe study has illustrated that ITN policies and interventions in Uganda need to be sensitive to community and region level factors that affect usage. Also, strategies to enhance women’s knowledge on malaria prevention is indispensable in improving ITN use.