Objectives To analyze evidence-based medicine (EBM) related projects funded by National Natural Science Foundation of China (NSFC) from 2000 to 2019. Methods The online NSFC database, Internet-based Science Information System, Biomart.cn, and MedSci.com were searched to obtain all EBM grants funded by NSFC. The achievements, Chinese papers and SCI-indexed papers, were obtained by searching the database of CNKI, VIP, SinoMed, WanFang Data and Web of Science. All data screened and extracted manually, and then managed and analyzed with Microsoft Excel 2016 software. Results The NSFC has funded 94 projects regarding EBM, with a total amount of 44.763 million Yuan (RMB) since 2000. Beijing, Shanghai, Guangdong and Sichuan ranked highly in the number of projects and their undertaking institutions and total amount of fundings. General programs and youth scientist programs constituted the main parts of fundings. The funded projects mainly originated from three subjects of new technologies and methods of TCM, health management and policy, clinical basis of integrated Chinese and western medicine. General programs contributed the most articles, while the distinguished young scientist programs had the highest average outputs. Three papers from Chinese EBM Center were published on BMJ and were highly cited. Conclusions Support of NSFC on EBM has increased continuously for the last twenty years, but it is still below the average. The fundings are unbalanced in areas and institutions. The supported research fields change every year, and show a trend of subjects aggregation.