Abstract Background Premature ejaculation (PE) is one of the most prevalent sexual dysfunctions in males. Repetitive transcranial magnetic stimulation (TMS) demonstrates potential modulatory effects on ejaculatory function, however, the effects of different stimulation frequencies remain unclear. Objectives To investigate the effects of low‐frequency and high‐frequency rTMS in a rat model of rapid ejaculation and compare these outcome with dapoxetine, a standard pharmacological intervention. Methods Male rats exhibiting rapid ejaculation were identified based on sexual behavior parameters, then randomly allocated into four groups: 1‐Hz rTMS, 10‐Hz rTMS, dapoxetine control, and sham control groups. Ejaculatory behavior, hippocampal 5‐hydroxytryptamine (5‐HT) levels, brain‐derived neurotrophic factor (BDNF) expression, and activation of the BDNF‐receptor tyrosine kinase receptor B (TrkB) pathway were investigated before and after 2 weeks of treatment. Results Following 2 weeks of intervention, we found that all rTMS and dapoxetine groups showed significant improvements in ejaculation latency compared with controls, with the 10‐Hz rTMS group showing the most substantial effect. While dapoxetine slightly outperformed 10‐Hz rTMS in increasing 5‐HT levels, 10‐Hz rTMS induced a greater upregulation of BDNF and TrkB expression. Correlation analysis revealed that BDNF levels were positively associated with EL ( r = 0.8817, p < 0.001) and negatively associated with ejaculation frequency ( r = –0.8702, p < 0.001). Conclusion rTMS exhibited frequency‐dependent therapeutic efficacy in rapid ejaculation rat models, with high‐frequency protocols demonstrating superior benefits compared with low‐frequency interventions. These effects are mediated through activation of the BDNF‐TrkB pathway and enhanced serotonergic signaling, suggesting high‐frequency rTMS as a promising non‐pharmacological therapy for PE.