OBJECTIVE: This research aims to comprehensively assess the efficacy of intermittent theta-burst stimulation (iTBS) vs. high-frequency repetitive transcranial magnetic stimulation (HF-rTMS) in post-stroke dysfunction. MATERIALS AND METHODS: Until January 2024, extensive electronic database searches were conducted (PubMed, Embase, Cochrane Library, Web of Science, etc.). Fugl-Meyer Assessment for Upper Extremities (FMA-UE) was used to assess upper limb (UL) dysfunction; post-stroke dysphagia (PSD) was identified by Standardized Swallowing Assessment (SSA), Fiberoptic Endoscopic Dysphagia Severity Scale (FEDSS), and Penetration/Aspiration Scale (PAS). Results were analyzed by network meta-analysis (NMA), and the mean difference (MD) and 95% confidence intervals (95% CI) were also reported. We conducted a descriptive analysis due to the inability to synthesize data on post-stroke cognitive impairment (PSCI). RESULTS: 19 studies were included for NMA analysis. For UL disorder, the efficacy of treatments was ranked as HF-rTMS [MD (95%CI):3.00 (1.69,4.31)], iTBS [MD (95%CI): 2.16 (0.84, 3.50)], and sham stimulation (reference). For PSD, the efficacy of treatment to reduce scores of FEDSS or SSA were iTBS [FEDSS, MD (95%CI): -0.80 (-1.13, -0.47); SSA, MD (95%CI): -3.37 (-4.36, -2.38)], HF-rTMS [FEDSS, MD (95%CI): -0.43 (-0.76, -0.10); SSA, MD (95%CI): -2.62 (-3.91, -1.35)], and sham stimulation(reference). Descriptive analysis of PSCI found that both iTBS and HF-rTMS were effective in improving PSCI. CONCLUSIONS: HF-rTMS demonstrates superior efficacy in UL dysfunction, while iTBS is more effective in PSD. Clinicians should carefully evaluate the type and severity of post-stroke dysfunction in each patient to select the most appropriate treatment.