Background: Numerous smoke-free tobacco or nicotine-containing product (TNP) alternatives have been introduced to support individual- and population-level harm reduction relative to continued cigarette smoking. This article details the nationwide prevalence and patterns of TNP use between 2016 and 2019 in Japan following the commercialization of IQOS™, a smoke-free heated tobacco product (HTP). Methods: Cross-sectional surveys were conducted over a period of three study years (2016/2017, 2017/2018, and 2018/2019) in representative samples of the Japanese general adult population and samples of Japanese adult IQOS users registered in the IQOS owner database of Philip Morris International’s affiliate in Japan. Results: Across the three study years (Y1-Y3), the prevalence of overall current TNP use (Y1-Y3: 18.5%, 18.9%, and 18.2%) and overall TNP use by age and sex remained similar. However, there was a growing shift from cigarette smoking to smoke-free TNP use across the three study years. While the cigarette smoking prevalence (Y1-Y3: 17.6%, 17.3%, and 16.0%) decreased, the use prevalence of smoke-free TNPs, including the HTP IQOS™ (Y1-Y3: 1.8%, 3.2%, and 3.3%) and e-cigarettes (Y1-Y3, 0.7%, 1.6%, and 2.0%) increased. At the same time, TNP initiation, TNP relapse, and TNP reinitiation with IQOS were all very low across the three study years. Across Y1-Y3, exclusive use of only one type of TNP (Y1-Y3: 82.3%, 75.0%, and 70.4%) decreased, while dual use of two types of TNPs (Y1-Y3: 14.3%, 17.2%, and 16.7%) increased, and poly-TNP use (Y1-Y3: 2.1%, 6.1%, and 10.0%) increased markedly. Moreover, the majority of adult IQOS users were exclusive IQOS users. Conclusions: These trends in IQOS use behavior suggest that IQOS™ has the potential to switch adult smokers from cigarettes to smoke-free tobacco products, which presents a harm reduction opportunity, and that HTPs are effective tools for complementing current tobacco control measures.