•The response trajectory was a logarithmic curve, suggesting that the depressive symptoms scores improved immediately in the first weeks, then gradually leveled off, and continued to be sustained afterward.•When separately examining active rTMS arms and sham rTMS arms, both response trajectories exhibited similar logarithmic curves. This implies that the sustained affect-effects of rTMS could not be explained only by a placebo effect.•The subgroup analyses show distinct response trajectories across different rTMS protocols. The 1-week stimulation group exhibited an inverted-U shaped curve, while the 4-week stimulation group showed a logarithmic curve.•The first two months of antidepressant outcome may be positively associated with rTMS protocols of higher pulse/session and total pulses The depression response trajectory after a course of repetitive transcranial magnetic stimulation(rTMS) remains understudied. We searched for blinded randomized controlled trials(RCTs) that examined conventional rTMS over left dorsolateral prefrontal cortex(DLPFC) for major depressive episodes(MDE). The effect size was calculated as the difference in depression improvement, between active and sham rTMS. We conducted a random-effects dose-response meta-analysis to model the response trajectory from the beginning of rTMS to the post-treatment follow-up phase. The area under curve (AUC) of the first 8-week response trajectory was calculated to compare antidepressant efficacy between different rTMS protocols. We included 40 RCTs(n = 2012). The best-fitting trajectory model exhibited a logarithmic curve(X2=17.7, P < 0.001), showing a gradual ascent with tapering off around the 3–4th week mark and maintaining until week 16. The maximum effect size was 6.1(95 %CI: 1.25–10.96) at week 16. The subgroup analyses showed distinct trajectories across different rTMS protocols. Besides, the comparisons of AUC showed that conventional rTMS protocols with more pulse/session group or more total pulses were associated with greater efficacy than those with fewer pulse/session or fewer total pulses, respectively. A course of conventional left DLPFC rTMS could lead to both acute antidepressant effects and sustained after-effects, which were modeled by different rTMS protocols in MDE.