Background Funding may impact the quality and findings of systematic reviews (SRs). We aimed to compare the methodological quality of funded and non-funded SRs that investigated the outcomes in ischemic stroke patients undergoing mechanical thrombectomy. Methods We conducted a comprehensive search strategy in different databases, including Ovid Cochrane Central Register of Controlled Trials, Ovid Embase, Ovid Medline (including epub ahead of print, in-process & other non-indexed citations), PubMed, Scopus and Web of Science Core Collection to retrieve all relevant SRs. Random sequence generation matched each funded SR with a non-funded one. A Measurement Tool to Assess Systematic Reviews (AMSTAR)-2 tool was used to assess the bias and quality of the included SRs. We also used uni- and multivariate analysis to perform our analysis, and results were expressed in odds ratio (OR) and 95% confidence interval (CI). Results We retrieved 150 articles, which were randomized and matched into 100 SRs, including 50 funded and 50 non-funded studies. By multivariate analysis, we found that including randomized clinical trials (RCTs) (OR: 5.7; 95% CI: 1.8–17.8; p = 0.003) and reporting conflict of interests (OR: 5.2; 95 CI: 1.1–24; p = 0.036) were the only significant differences between funded and non-funded SRs. No significant differences were found regarding the overall confidence for low-quality (OR: 0.54; 95% CI: 0.09–3.2; p = 0.49) and moderate/high-quality SRs (OR: 0.17; 95% CI: 0.02–1.87; p = 0.14). Conclusion Funded studies tend to include RCTs more often and report conflict of interests with no significant impact on overall confidence.