PURPOSE: This study aimed to evaluate the efficacy of repetitive transcranial magnetic stimulation (rTMS) in treating lower limb motor dysfunction after stroke and explore the optimal stimulation parameters. METHODS: PubMed, Embase, Cochrane Library, and other relevant databases were systematically queried for randomised controlled trials (RCTs) investigating the efficacy of rTMS in addressing lower limb motor dysfunction post-stroke. The search encompassed records from inception to July 2022. The assessed outcomes encompassed parameters such as the Fugl-Meyer motor function score for lower limbs, balance function, and Barthel index (BI). Three independent researchers were responsible for research selection, data extraction, and quality assessment. Study screening, data extraction, and bias evaluation were performed independently by two reviewers. Data synthesis was undertaken using Review Manager 5.3, while Stata version 14.0 software was employed for generating the funnel plot. RESULTS: A total of 13 studies and 428 patients were included. The meta-analysis indicated that rTMS had a positive effect on the BI (MD = 5.87, 95% CI [0.99, 10.76],  = 0.02, I2 = 86%, of studies = 8, of participants = 248). Subgroup analysis was performed on the stimulation frequency, treatment duration, and different stroke stages (stimulation frequency was low-frequency (LF)-rTMS (MD = 4.45, 95% CI [1.05, 7.85],  = 0.01, I2 = 0%, of studies = 4, of participants = 120); treatment time ≤ 15 d: (MD = 4.41, 95% CI [2.63, 6.18],  < 0.00001, I2 = 0%, of studies = 4, of participants = 124); post-stroke time ≤6 months: (MD = 4.37, 95% CI [2.42, 6.32],  < 0.0001, I2 = 0%, of studies = 5, of participants = 172). CONCLUSION: LF-rTMS had a significant improvement effect on BI score, while high-frequency (HF)-rTMS and iTBS had no significant effect. And stroke time ≤6 months in patients with treatment duration ≤15 d had the best treatment effect.