The current study aimed to assess the prevalence of obesity and to explore the relationship between socioeconomic status and obesity among adolescents in Taiwan, a transitioning country. Data from the Taiwan School Physical Fitness Database on 1,875,627 Taiwanese adolescents aged 10-18 years were analyzed. The average family income per household in each district was collected from the national statistical institutional database. Descriptive statistics, Chi-square tests, Pearson correlation analysis, and mixed model analyses were used. The overall prevalence of combined overweight and obesity was 28.1%. The prevalence of overweight/obesity significantly differed according to gender and age. Furthermore, the average family income per household was negatively associated with the district-level prevalence of obesity. Additionally, when controlling for physical fitness, the average family income per household remained negatively associated with adolescent obesity. In addition, multilevel analysis was also applied to explore the relationship between district-level socioeconomic status and individual-level obesity to prevent the nested data structure from affecting the results. The results revealed that the average family income per household negatively correlated with individual obesity. These findings provide insight for public health officials into preventing and managing adolescent obesity.