This study investigated the heterogeneity of depressive symptom trajectories and the roles of school-related factors in predicting the membership of different trajectories in a sample of early adolescents in Taiwan. In all, 870 junior high school students were followed for 3 years. Using growth mixture modeling, the study identified four distinct trajectories: stable-low depression, stable-moderate depression, steadily increasing depression, and early elevated but later decreasing depression. Female and private school students tended to belong to the high-risk group. Students with negative academic self-concept, low self-esteem, or poor peer relationships tended to follow the two high-risk trajectories (stable-moderate depression and steadily increasing depression). The findings suggested that these school-related factors could be used to target the high-risk depressive symptom groups for receiving further counseling, especially in the East Asian context.