Background: In the Korean educational system, academic achievement is one of the crucial factors in assessing a student's academic ability for postsecondary education. Thus, many researchers have been studying ways to improve students' academic achievement. Objective: The purpose of this study was to examine the relationship between students' perceptions of teachers' motivational behavior and students' academic achievement, as well as the mediating effects of students' motivation and self-efficacy on this relation. Methods: Using the Korean Education Longitudinal Study data, we employed structural equation modeling to assess the impacts of different variables (i.e., students' perceptions of their teachers' motivational behavior, self-efficacy, and intrinsic motivation) on the academic achievements of 6227 middle school students'. We further examined whether these relationships differed depending on the school subject, specifically, reading, English, and mathematics. Results: The results indicate that students' self-efficacy and intrinsic motivation mediated the relation between students' perceptions of teachers' motivational behavior and students' academic achievements in all three subjects. Conclusion: This study suggests that students' self-efficacy and intrinsic motivation increase when students perceive their teachers' motivational behaviors positively, which ultimately improves their performance in reading, English, and mathematics.