Herbal and 'natural' products are a growing industry in today's society because they reportedly help with numerous diseases and ailments. To date, there are some randomised controlled trials (RCTs) conducted on patients concerning the efficacy of flavonoids against viral acute respiratory tract infection (ARTI) showing inconsistent results. On this basis, we will summarise the available evidence to investigate the efficacy of flavonoids on viral ARTI by conducting a systematic review and meta-analysis.This protocol has been registered. The systematic review and meta-analysis will be conducted by Cochrane guidelines and reported according to the Preferred Reporting Items for Systematic Review and Meta-Analysis statement. RCTs comparing the flavonoids group with the control group for treating virus-induced ARTI will be included. RCTs published with relative outcomes will be searched through 12 databases. Data were searched from inception to 25 March 2022. Relevant literature search, data extraction and quality assessment will be performed by pairs of reviewers independently, and the third researcher will be involved in a discussion for disagreements. Stata V.16.0 software will be used for statistical analysis. Dichotomous data will use the ORs with 95% CIs. Continuous data will use the weighted mean difference with 95% CIs. Heterogeneity will be tested by χ2-based Cochran Q statistic and I2 statistic. Sensitivity analyses and subgroup analyses will be used to observe the heterogeneity between included studies. The funnel plot, Egger's test and Begg's test will be used to judge the publication bias. A p<0.05 will be considered to indicate a statistically significant result.INPLASY202180107.© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.