Background: In the context of declining smoking rates in Estonia, this study aims to analyze the recent trends in e-cigarette use and its associations with smoking status and sociodemographic factors. Methods: Nationally representative data from biennial cross-sectional health surveys in 2012–2018 (n = 9988) were used to describe the prevalence of smoking and e-cigarette use by smoking status in Estonia. Multivariate logistic regression analysis was used to describe the sociodemographic patterns of e-cigarette use in three subgroups: the general population, smokers, and ex-smokers. Results: The prevalence of current smoking decreased from 45.4% in 2012 to 31.5% in 2018 among men and from 26.6% to 20.0% among women. At the same time, e-cigarette use in the general population had increased to 3.7% among men and to 1.2% among women. The increase in the prevalence of e-cigarette use was statistically significant among men in the general population, smokers, and ex-smokers, but non-significant among women. In addition to period effects, e-cigarette use was patterned by age, gender, and education. Conclusion: In 2002–2018, the e-cigarette use had increased but smoking had decreased in Estonia. A timely and targeted tobacco policy may alleviate the harm of e-cigarette use from the public health perspective.