The COVID-19 pandemic is predicted to affect adolescent smoking behaviours. We aim to map profiles of adolescents’ smoking behaviours in a rural district in Indonesia during the COVID-19 pandemic and validate their smoking exposures using cotinine tests. This study applied an online survey followed by cotinine tests for high-school students in Gunung Kidul, Yogyakarta. The participants were asked to complete the survey and participate in a cotinine test. Univariate and multivariate regressions were performed to seek potential determinants of the smoking status and diagnostic accuracy of the cotinine test. A total of 281 participants completed the survey, with 19.6% (n = 55) and 22.8% (n = 64) being ever-smokers and current smokers. The impacts of the pandemics on their smoking behaviours were found in the urgency and numbers of daily smoked cigarettes. Univariate regression analysis revealed age, gender, learning mode, and whether father/friend smokes correlate with the adolescents’ smoking behaviours. Multivariate regression analysis revealed that the odds of planning to stop smoking were 0.01 (95% CI 0.001–0.22, p-value 0.003) for having positive attitudes towards cigarettes compared to none. Of the 65 cotinine tests, 19 tested positive, with the sensitivity and specificity of the cotinine test at 94.7% and 95.6%. The prevalence of adolescent smoking during the COVID-19 pandemic in Gunung Kidul is high, with the impacts of the pandemic on the urgency and number of cigarette smoke. There are opportunities to help them stop smoking by providing reliable quit-tobacco access and advocacy in collaboration with schools, parents, and health providers.