Adolescent overweight and obesity are growing public health concerns in developing nations like Ethiopia. They are closely linked to an increased risk of non-communicable diseases, a deterioration in health-related quality of life, subpar academic performance, and a decline in social and emotional well-being. There is, however, little research in this field. Thus, this study aimed to assess overweight and obesity and associated factors among public and private secondary school adolescent students in Harar city, Eastern Ethiopia. A school-based comparative cross-sectional study was conducted among 781 secondary school adolescents in Harar city from February to March 2022. Multi-stage sampling was used to identify 781 study participants (586 in public and 195 in private schools). Anthropometric measures and self-administered structured questionnaires were used to obtain the data. Bivariate and multivariate logistic regression were used to determine the association between independent variables and overweight and obesity. Statistical significance was declared at P < .05. The overall magnitude of overweight and obesity was 9.3% [95% confidence interval (CI) = 7.2-11.4%] with 16.2% in private schools. Being female [adjusted odd ratio (AOR) = 2.04, 95% CI: 1.17-3.55], late adolescent age [AOR = 0.53, 95% CI: 0.31-0.90], bigger family size [AOR = 0.55, 95% CI: 0.31-0.97], high paternal education level [AOR = 2.03, 95% CI: 1.08-3.81], eating meat [AOR = 3.41, 95% CI: 1.27-9.17] and not consuming breakfast daily [AOR = 2.13, 95% CI: 1.24-3.67] were factors associated with overweight and obesity among all secondary school adolescents. A high maternal educational level, not eating breakfast and dinner daily in private secondary school adolescents and having a feminine gender, eating eggs, and not walking or riding a bicycle for at least 10 minutes continuously in public secondary school adolescents were factors associated with overweight and obesity. The extent of overweight and obesity was notably higher in the study area. Communities and educational institutions should work together to promote healthy lifestyle choices among adolescents, with a special emphasis on girls and students enrolled in private schools.