Objectives: Cigarette smoking prevalence among adolescent males in rural areas of Korea has increased in recent years. The aim of this study was to explore the factors related to increasing trends in cigarette smoking among adolescent males living in rural areas. Methods: The raw data from the Korea Youth Risk Behavior Web-based Survey from 2006 to 2009 were used. Data were analyzed by using the method of complex survey data analysis considering complex sampling design. Multiple logistic regression models were used to explore the factors affecting cigarette smoking. We evaluated the linear time trends in the prevalence of factors that were related to current smoking status and the linear time trends in cigarette smoking in groups stratified by the exposure to each factor using logistic regression models. Finally, we examined the contributions of the factors to the time trends in cigarette smoking by adjusting for each of those factors in the baseline regression models and changes in the adjusted odds ratio by survey year. Results: A statistically significant increasing trend in smoking was observed after adjusting for the factors affecting cigarette smoking. Significant factors related to cigarette use were perceived stress, experience with depression, current alcohol drinking, exposure to secondhand smoke, and academic performance. The factor related to increasing trends in cigarette smoking was academic performance. Conclusions: Stress about academic performance is an important factor affecting the increase in cigarette smoking among adolescent males in a rural area of Korea.