Background: In recent years, the potential of non-invasive brain stimulation (NIBS) for therapeutic effects on cognitive functions has been explored for populations with stroke. There are various NIBS methods depending on the stimulation site and stimulation parameters. However, there is no systematic NIBS review of post-stroke cognitive impairment with a focus on stimulation sites and stimulation parameters. The purpose of this study is to conduct a systematic review and meta-analysis on effectiveness and safety of NIBS for cognitive impairment after a stroke to obtain new insights. This study was prospectively registered with the PROSPERO database of systematic reviews (CRD42020183298). Methods: All English articles from MEDLINE, Scopus, CINAHL, Embase, PsycINFO, and CENTRAL were searched from inception up to 31 December 2020. Randomized and prospective controlled trials were included for the analysis. Studies with at least five individuals post-stroke, whereby at least five sessions of NIBS were provided and using standardized neuropsychological measurement of cognition, were included. We assessed the methodological quality of selected studies as described in the Physiotherapy Evidence Database (PEDro) scoring system. Results: A total of 10 studies met eligibility criteria. Six studies used repetitive transcranial magnetic stimulation (rTMS) and four studies used transcranial direct current stimulation (tDCS). The pooled sample size was 221 and 196 individuals who received rTMS and tDCS respectively. Eight studies combined general rehabilitation, cognitive training, or additional therapy with NIBS. In rTMS studies, target symptoms included global cognition (n = 4), attention (n = 3), memory (n = 4), working memory (WM) (n = 3), and executive function (n = 2). Five studies selected the left dorsolateral prefrontal cortex (DPLFC) as the stimulation target. One rTMS study selected the right DLPFC as the inhibitory stimulation target. Four of six studies showed significant improvement. In tDCS studies, target symptoms included global cognition (n = 2), attention (n = 4), memory (n = 2) and WM (n = 2). Three studies selected the frontal area as the stimulation target. All studies showed significant improvement. In the meta-analysis, rTMS showed a significant effect on attention, memory, WM and global cognition classified by neuropsychological tests. On the other hand, tDCS had no significant effect. Conclusions: In post-stroke patients with deficits in cognitive function, including attention, memory, and WM, NIBS shows promising positive effects. However, this effect is limited, suggesting that further studies are needed with more precision in stimulation sites and stimulation parameters. Future studies using advanced neurophysiological and neuroimaging tools to allow for a network-based approach to treat cognitive symptoms post-stroke with NIBS are warranted.