Using data from the Analysis on the Actual Status and its Level of School Education, this study examined the influence of teacher-centered and learner-centered instruction on students’ academic achievement. Quantile regression was employed to account for the differential effect of teaching methods by achievement levels. The results indicated that teacher-centered lecture style had a positive impact on every quantile of student achievement in every subject. The lecture style was found to be more effective for students with low achievement quantile in Korean and English as for high achieving students. Student-centered discovery and inquiry teaching, however, had a negative impact on academic achievement in general, and for low achieving students in particular. Also, student-centered discussion method had a negative impact on students with low quantile and high quantile achievement in Korean and English. This study, which empirically confirmed the differential effect of teaching methods by achievement levels, discusses the need to expand educational support in order to improve teaching methods for students with different academic performances.