<p>Academic alienation presents a significant educational challenge. Shyness, viewed as a temperamental disposition, could potentially play a crucial role in fostering academic alienation. However, there is still a lack of longitudinal studies that fully uncover the relationship between shyness and academic alienation, as well as the mediating mechanisms underlying this relationship. The current study aimed to test the longitudinal relationship between shyness and academic alienation, as well as the mediating role of peer exclusion. A three-wave longitudinal study was conducted over three years, involving 1265 early adolescents with a mean age of 9.59 (<i>SD</i> = 0.60), of whom 49.8% were girls. Cross-lagged modeling was employed to test longitudinal relationships and mediating mechanisms. The findings indicated that: (a) T1 shyness positively predicted T2 academic alienation; (b) peer exclusion mediated the relationship between shyness and academic alienation; (c) peer exclusion and academic alienation showed a mutually predictive relationship. These findings offer new insights into the intricate mechanisms linking shyness with academic alienation. They also have important theoretical implications for guiding educational practices and developing school-based intervention programs aimed at enhancing adolescent success in education and future endeavors.</p>