Background: Peer victimization is ubiquitous across schools and cultures, and has the potential for long-lasting effects on the well-being of victims. To date, research has focused on the consequences of peer victimization during childhood but neglected adolescence. Peer relationships and approval become increasingly important during adolescence; thus, peer victimization at this age may have a damaging psychological impact. Methods: Participants were 5030 adolescents aged 11–16 recruited from secondary schools in the UK. Self-report measures of victimization and symptoms of anxiety and depression were administered on three occasions over a 12-month period. Latent growth models examined concurrent and prospective victimization-related elevations in anxiety and depression symptoms above individual-specific growth trajectories. Results: Peer victimization was associated with a concurrent elevation of 0.64 and 0.56 standard deviations in depression and anxiety scores, respectively. There was an independent delayed effect, with additional elevations in depression and anxiety (0.28 and 0.25 standard deviations) six months later. These concurrent and prospective associations were independent of expected symptom trajectories informed by individual risk factors. Conclusions: Adolescent peer victimization was associated with immediate and delayed elevations in anxiety and depression. Early intervention aimed at identifying and supporting victimized adolescents may prevent the development of these disorders.