Objective To systematically evaluate the effect of intermittent theta burst stimulation (iTBS) on lower extremity motor function and balance function in patients with stroke. Methods A systematic literature search was conducted in the Cochrane Library, Embase, PubMed, Web of Science, CNKI, SinoMed, Wanfang data and VIP from inception to February 19, 2025. Randomized controlled trials comparing iTBS with conventional rehabilitation or sham iTBS in patients with post-stroke lower extremity motor and balance dysfunction were included. The methodological quality of the included studies was assessed using the Cochrane Risk of Bias Tool. Meta-analysis was performed using RevMan 5.4 and Stata 14.0. Results A total of 16 articles involving 647 patients were included. Meta-analysis showed that iTBS improved the Fugl-Meyer Assessment-Lower Extremities score (MD = 2.58, 95%CI 1.61 to 3.55, P < 0.001), Berg Balance Scale score (MD = 4.11, 95%CI 2.43 to 5.79, P < 0.001), Barthel Index score (MD = 4.95, 95%CI 0.97 to 8.92, P =0.010) and motor-evoked potential (MEP) latency (MD = -1.42, 95%CI -2.54 to -0.30, P = 0.010). Subgroup analyses suggested that at subacute stage, cerebellar iTBS, more than ten treatment sessions, and 1 200 pulses per day may be more effective. Conclusion iTBS may improve lower extremity motor function and activities of daily living in patients with stroke, and shorten MEP latency, and it may also confer potential benefits in improving balance function in these patients.