This study attempted to clarify whether the pattern of academic achievement between genders changed due to the online school opening conducted after COVID-19, and whether there was a interaction effect of subject self-efficacy at this time. To this end, the 2020 data of the National Assessment of Educational Achievement organized by the Korea Institute of Curriculum and Evaluation were used and analyzed for middle school levels to which the national common curriculum was applied. The analysis method used a multilayer model (HLM), and the main results of this study are presented as follows. First, it is worth noting that after COVID-19, female students' academic achievement was higher than that of male students in all subject areas, which showed the same tendency even in mathematics, which was previously reported for male students to be higher. Second, the interaction effect of subject self-efficacy in the influence of academic achievement according to gender was significant in the overall subject average and English subject. Third, as a result of additional analysis to compare the influence of each variable for each male and female group, it was found that male students had a greater influence on subject learning motivation and independent study hours than female students. Based on these research results, policy implications for reducing the educational gap between genders were presented.