Meta-analysis results indicated that rTMS within NIBS significantly improved the Pittsburgh Sleep Quality Index (PSQI) score (MD = −1.85, 95% CI [−2.99, −0.71], p < 0.05), the 17-item Hamilton Depression Rating Scale (HAMD-17) score [MD = −2.85, 95% CI (−3.40, −2.30), p < 0.05], and serum brain-derived neurotrophic factor (BDNF) levels [MD = 4.19, 95% CI (2.70, 5.69), p < 0.05], while reducing the incidence of adverse reactions [RR = 0.36, 95% CI (0.23, 0.55), p < 0.05]. This evidence concerns the gene BDNF and major depressive disorder.