Background <p>Our previous study demonstrated that continuous theta burst stimulation (cTBS) may enhance motor recovery but did not significantly improve pushing behavior in patients with poststroke lateropulsion, necessitating a novel repetitive transcranial magnetic stimulation (rTMS) protocol. Furthermore, the cortical hemodynamic mechanisms underlying postural recovery remain unexplored, limiting insight into how rTMS modulates posture-related neuroplasticity in this population.</p> Methods <p>A randomized, three-arm, patient- and assessor-blinded sham-controlled trial was conducted. Forty-two eligible participants with poststroke lateropulsion were randomly assigned to receive either cTBS or high-frequency rTMS or sham rTMS for 3&#xa0;weeks. Primary outcomes were Burke lateropulsion scale and scale for contraversive pushing. Secondary outcomes included short falls efficacy scale international, modified Rivermead mobility index, Fugl-Meyer assessment scale-motor domain, and stroke-specific quality of life scale. Cortical hemodynamics were monitored via functional near-infrared spectroscopy over ten posture-related cortices.</p> Results <p>A significant main effect of time was observed on Burke lateropulsion scale (BLS) (<i>F</i> = 21.8, <i>P</i> &lt; 0.001), scale for contraversive pushing (<i>F</i> = 16.5, <i>P</i> &lt; 0.001), short falls efficacy scale international (<i>F</i> = 16.3, <i>P</i> &lt; 0.001), modified Rivermead mobility index (<i>F</i> = 26.2, <i>P</i> &lt; 0.001), and Fugl-Meyer assessment scale-motor domain (<i>F</i> = 13.6, <i>P</i> &lt; 0.001). In the subgroup analysis, a significant difference on BLS was observed at T3 between the cTBS and Sham rTMS groups in patients with mild-moderate lateropulsion [− 2.4 (− 4.6, − 0.3), <i>P</i> = 0.026]. Regarding posture-related cortical hemodynamics, a significant three-way interaction was observed in the left dorsolateral prefrontal cortex for the mean difference in oxygenated hemoglobin between sitting task and baseline rest (<i>F</i> = 3.9, <i>P</i> = 0.012). However, no significant main effects of time or intervention were detected in this cortex. Multiple linear regression analyses revealed no significant linear relationship between mean difference in oxygenated hemoglobin from sitting task to baseline rest (T3–T0) across ten cortices and either BLS (T3–T0) (<i>R</i>² = 0.189, <i>P</i> = 0.699) or SCP (T3–T0) (<i>R</i>² = 0.272, <i>P</i> = 0.355).</p> Conclusions <p>cTBS significantly improved the pushing behavior in patients with mild-moderate lateropulsion. These findings support the efficacy of rTMS in improving poststroke lateropulsion and provide a foundation for future studies aimed at optimizing rTMS protocol targeting this condition.</p> Trial registration <p>URL: <a href="http://www.chictr.org.cn">http://www.chictr.org.cn</a>.; Unique identifier: ChiCTR2300068243.</p>