Repetitive transcranial magnetic stimulation (rTMS) is an effective therapy for acute treatment of major depressive disorder (MDD). However, the efficacy and optimal strategy of delivering maintenance rTMS beyond acute treatment remains unclear. This meta-analysis aims to quantify the treatment effect of maintenance rTMS therapy in MDD and compares the difference in treatment effect between the fixed and rescue maintenance rTMS protocols. We conducted a meta-analysis of 14 studies (N = 705) comparing depression rating scores before and after maintenance rTMS. Standardized mean scores adjusted for sample size (Hedges g) were used as the effect size. Subgroup analysis was performed to compare the fixed and rescue maintenance rTMS treatment. Maintenance rTMS was associated with a statistically significant improvement in depression scores (standardized mean difference [SMD] = 0.75; confidence interval [CI] = -1.25 to -0.25). The random effects model had the Q value = 142.67 (P < 0.0001) and I2 = 90%, supporting significant heterogeneity among studies. The prediction interval yielded a possible effect size from -2.54 to 1.05. The subgroup analysis showed a stronger treatment effect for rescue maintenance protocol (SMD = -1.17; CI = -2.13 to -0.21) compared to fixed maintenance protocol (SMD = -0.45; CI = -1.00.16). Although not statistically significant (Q-between = 2.56, df-between = 1, P = 0.1096), a large difference in effect size was observed between subgroups. Maintenance rTMS appears to be an effective strategy for maintaining remission and preventing relapse in MDD. Significant heterogeneity among the studies warrants caution in interpreting the results. These findings suggest the need for standard protocols and consensus guidelines for the optimal delivery of maintenance rTMS treatment.