Stroke is a significant global cause of mortality and morbidity, and post-stroke cognitive impairment (PSCI) affects up to half of stroke patients. Despite the availability of pharmacological and non-pharmacological interventions, there is a lack of definitive effective treatments for PSCI. Non-invasive brain stimulation, particularly intermittent theta burst stimulation (iTBS), has emerged as a promising therapy for the treatment of PSCI. This systematic review and meta-analysis aimed to evaluate the efficacy and safety of iTBS in enhancing cognitive function among patients with PSCI. A comprehensive search was conducted across multiple databases, including PubMed, Web of Science, Scopus, Cochrane Library, and CNKI, to identify relevant randomized controlled trials published before April 2023. The primary outcome measured changes in global cognitive scales, while the secondary outcomes focused on improvements in attention, orientation, visual-spatial perception, and activities of daily living. The meta-analysis encompassed six studies involving 325 patients. The results demonstrated that iTBS led to a significant improvement in global cognitive scales (SMD = 1.12, 95% CI = [0.59 to 1.65], P < 0.0001), attention (SMD = 0.48, 95% CI [0.13 to 0.82], P = 0.007), visual perception (SMD = 0.99, 95% CI [0.13 to 1.86], P = 0.02), and activities of daily living (SMD = 0.82, 95% CI [0.55 to 1.08], P < 0.00001). However, there was no significant effect on orientation (SMD = 0.36, 95% CI [- 0.04 to 0.76], P = 0.07). Subgroup analysis based on the number of sessions was conducted, revealing a significant improvement in global cognition among patients with PSCI across the three categories (10 sessions, 20 sessions, and 30 sessions) with no between-group difference (P = 0.28). None of the included studies reported any serious adverse effects. In conclusion, iTBS appears to be a safe and effective non-invasive treatment that can enhance the cognitive abilities and daily living skills of patients with post-stroke cognitive impairment. However, our conclusion is constrained by the limited number of studies. Further high-quality, large-sample RCTs with extended follow-up periods are necessary to validate these findings. Integrating iTBS with brain imaging techniques, such as functional near-infrared spectroscopy and functional magnetic resonance, could aid in understanding the mechanism of iTBS action.