OBJECTIVES: This study aimed to evaluate the efficacy of different repetitive transcranial magnetic stimulation (rTMS) modes in stroke patients with cognitive impairment, and to rank the best option according to the outcome measures. METHODS: Literature was searched in PubMed, Cochrane Library, Web of Science, Embase, SinoMed, China National Knowledge Infrastructure, Wanfang Database, and VIP Database, from database inception to September 2023. We included randomized controlled trials (RCTs) investigating the efficacy of all rTMS modes for post-stroke cognitive impairment. The selected studies assessed at least one of the following outcome measures: Montreal Cognitive Assessment (MoCA), Mini-Mental State Examination (MMSE), P300 latency and amplitude, and modified Barthel Index (MBI) or BI. Two researchers independently conducted data extraction. Quality assessment was performed using RevMan 5.3 software based on the Cochrane Collaboration's tool, and statistical analysis was conducted by GeMTC 0.14.3 software and Stata 17.0 software. RESULTS: The network meta-analysis included 74 RCTs with a total of 5478 patients. The best probability ranking indicated that intermittent theta burst stimulation (iTBS) was the most effective in enhancing MoCA, MMSE and MBI scores (85%, 54%, 42%, respectively), followed by 10 Hz rTMS (79%, 50%, 39%, respectively), for P300 amplitude, ≤1 Hz rTMS was ranked first (52%). CONCLUSIONS: The current limited evidence suggests that iTBS may be the optimal approach for improving cognitive and daily life abilities of stroke patients, followed by 10 Hz rTMS, ≤1 Hz rTMS may be the preferred option for enhancing P300 amplitude. TRAIL REGISTRATION: PROSPERO 2023 CRD42023424771 available from: https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=424771.