Peer relationship difficulties are strongly correlated with aggressive behaviors among adolescents in cross-sectional studies. However, effects of aggressive behaviors on peer relationship difficulties are known to be inconsistent. Longitudinal reciprocal effects between these two variables are currently unclear. Using data from the Korean Children and Youth Panel Survey from 2011 to 2013, this study investigated longitudinal reciprocal effects between these two variables in Korean adolescents. Participants were 2,280 second-grade middle school students (eighth graders in the USA) at Time 1. Results from autoregressive cross-lagged model showed that peer relationship difficulties and aggressive behaviors were stable over a three-year period while longitudinal effects between these two variables were mutually and positively significant. However, the impact of peer relationship difficulties on aggressive behaviors was greater than that of the opposite (i.e., the impact of aggressive behaviors on peer relationship difficulties). Findings of this study suggest that schools should focus on preventive education and counseling for adolescents' peer relationship problems and aggressive behaviors. Furthermore, inservice trainings for teachers and counselors focusing on enhancing their understandings of these reciprocal relationships may help students improve peer relationship while reducing aggressive behaviors.