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A prolonged repetitive transcranial magnetic stimulation (rTMS) treatment course could be beneficial for some patients experiencing major depressive episodes (MDE). We identified trajectories of rTMS response in depressive patients who received an extended rTMS treatment course and sought to determine which trajectories achieved the greatest benefit with a prolonged treatment course. We applied group-based trajectory modeling to a naturalistic dataset of depressive patients receiving a prolonged course of sequential bilateral rTMS (up to 51 treatment sessions) to the dorsolateral prefrontal cortex. Trajectories of the PHQ-9 with extended treatment courses were characterized, and we explored the association between baseline clinical characteristics and group membership using multinomial logistic regression. Among the 324 study participants, four trajectories were identified: "linear response, extended course" (N = 73; 22.5 %); "nonresponse" (N = 23; 7.1 %); "slowed response" (N = 159; 49.1 %); "rapid response, standard treatment length" (N = 69; 21.3 %). Only the "linear response, extended course" group showed considerable clinical improvement after receiving additional rTMS treatments. Greater baseline depressive symptoms were associated with linear response and non-response. Our results confirmed the distinctive response trajectories in depressive patients receiving rTMS and further highlighted that prolonged rTMS treatment courses may be beneficial for a subset of patients with higher initial symptom levels and linear early treatment response. • A moderate proportion of patients could benefit from the prolonged treatment course. • The baseline symptom severity predicts the membership of this subgroup. • We identified four trajectories of response, replicating our previous findings. [ABSTRACT FROM AUTHOR]