Anemia is associated with physical, cognitive, and developmental problems. Given that there are limited studies on anemia prevalence among obese Asian adolescents and that past evidence is controversial, this study investigated the relationship between obesity and anemia in a nationally representative sample of South Korean adolescents. Data were obtained from the 2007–2019 Korea National Health and Nutrition Examination Survey. Overall, 10,231 subjects were included in the analysis. Multiple logistic regression was performed to determine the relationship between obesity and anemia. Compared with the non-obesity group, the adjusted odds ratio (OR; 95% confidence interval [CI]) of anemia was 1.00 (0.66–1.50) in the obesity group. However, in the early adolescent subgroup of 10–13 years (adjusted OR, 2.88; 95% CI, 1.20–6.95), the risk of anemia was significantly higher in the obese group than in the non-obese group. Obesity was associated with an increased risk of anemia in early adolescents. Obese adolescents aged 10–13 require special care, especially through regular examination and management for anemia.