Objective To describe the prevalence of use of electronic nicotine delivery systems (ENDS) and waterpipe in Brazil, by population subgroups, and to evaluate the trend between 2013 and 2019. Methods We used data from the 2019 National Health Survey to estimate the prevalence of lifetime and current use of ENDS and current use of waterpipes by socio-behavioral characteristics. Differences in prevalence over time were calculated using data from the III Brazilian Household Survey on Substance Use-2015 and the National Health Survey-2013. Results For 2019, the prevalence of current use of ENDS was estimated at 0.64% (∼1 million people), of which ∼70% were in the age group of 15–24 years old. The highest prevalence was observed in the Midwest region, but the Southeast region concentrates half of these users. Almost 90% are non-smokers, with high prevalence among those who also use waterpipe and abuse alcohol. There was an increase in ENDS use between 2015 and 2019, particularly among younger people. The prevalence of current waterpipe use in 2019 was estimated at 0.47% (∼800,000 individuals), of which ∼80% were 15–24 years old. There was an increase in the prevalence of current waterpipe use between 2013 and 2019, and among young people the increase was ∼300%. Conclusions In Brazil, ENDS have been used mostly by young people, and by never smokers of manufactured cigarettes. The use of ENDS and waterpipe has been increasing even with the country’s regulatory restrictions, which may compromise the successful history of the tobacco control policy.