According to the basic psychological needs theory of the self-determination theory, school climate can be regarded as a context that enables an individual’s psychological growth. Moreover, when the psychological growth such as self-resilience is achieved through the school climate, the self-directed learning level of adolescents can, theoretically, be improved in the learning field. To verify these theoretical assumptions, we applied the latent growth curve modeling analysis on 4th to 6th waves of data (4th grade of elementary school panel of Seoul Education Longitudinal Study) and investigated the relations among middle school students’ ratings on the school climate, the trajectories of the self-resilience level, and the self-directed learning level. The main results are as follows. First, the students’ self-resilience level decreased through 4th to 6th waves. Also, there were individual differences in this declining tendency. Second, as the adolescents perceived the school climate more positively, their self-resilience and the self-directed learning level increased. In addition, the self-directed learning level was found to be higher as the slope of self-resilience decreased slowly. The results of this study show that the school climate and the self-resilience of middle school students were important factors for improving the level of students’ self-directed learning. Based on these results, we suggest several implications for improving the level of student’s self-directed learning for the schools and other related organizations.