Drawing on first to fourth wave data from the Busan Education Longitudinal Study(BELS), we explored the effects of Busan-type innovative schools on students’ cognitive and affective achievements, and examined the differences in characteristics between early innovative schools and those designated later, using panel analysis and difference in differences(DID). Results exhibited that initially, the average academic achievement level of innovative school students was slightly lower than that of general school students, but the difference narrowed and reached a similar level as the grade level went up. Students' school satisfaction declined as the grade level went up, but the trend of decline in innovative schools was milder than that of general schools. In affective achievements such as creativity, academic self-efficacy, and a sense of community, no significant difference was found between innovative schools and general schools. On the other hand, those schools that were recently converted to innovative schools showed higher academic achievement than other schools when they were formerly general schools, but after the transition to innovative schools, they attained a level of achievement that was not much different from other schools. Based on the results, we assessed the performance of the Busan-type innovative schools and discussed policy alternatives for improving innovative schools.