The effectiveness of a peer-led education intervention in HIV/AIDS prevention was assessed in the Chinese children of migrant workers. A prospective study was conducted in 12 junior high schools for migrant children. Among the intervention group, a peer-education-based HIV/AIDS prevention was implemented for three months. The results during the baseline survey indicated that the level of knowledge on HIV/AIDS was lower in children of migrant workers. After three months of peer-led intervention, compared with the control group, students in the intervention group positively increased their HIV/AIDS-related knowledge, modified their attitude and improved their protection self-efficacy. Compared with attitude, intervention was more effective in the improvement of knowledge and protection self-efficacy, especially knowledge. The findings suggest that peer-led education was an effective method in improving knowledge, attitude and protection self-efficacy in Chinese children of migrant workers. Heightened concerns targeting the group students were particularly necessary, given their lower level of related knowledge and vulnerability to HIV infection.