An atypical Cortisol Awakening Response (CAR) has been related to adult anxiety and depression, but little is known about the association between long-term atypical CAR and adolescent anxiety and depression. This study aimed to longitudinally identify subgroups of adolescents with distinct levels of CAR (i.e., adolescents with and without persistent atypical CAR) and to examine their development of anxiety and depressive symptoms over 3 successive years. A community sample of 184 Dutch adolescents (M age = 14.99 at T1, 57 % boys) completed annual salivary cortisol assessments at home at time of awakening, and 30 and 60 min post-awakening (i.e., CAR) for 3 successive years. Adolescents also reported annually on their anxiety and depressive disorder symptoms. Latent Class Growth Analysis suggested two subgroups of adolescents with respect to CAR: a “low” group with stable low levels of AUCg (Area Under the Curve with respect to the ground) over time and a “high” group with high and increasing levels of AUCg over time. Controlling for sex, the high and low CAR groups significantly differed in depressive symptoms only, but none of the anxiety disorder symptoms. More specifically, adolescents in the high CAR group showed significantly higher mean levels of depressive symptoms over time compared to adolescents in the low CAR group. These results suggest that persistent heightened CAR is a more consistent, yet modest, correlate of adolescent depressive symptoms than anxiety disorder symptoms.