Reliable estimates of the prevalence of food allergy (FA) among the general Chinese population have remained unclear. This meta-analysis aims to provide an accurate estimate of FA prevalence in China with comprehensive data. A systematic literature search was conducted in eight electronic databases, i.e., China National Knowledge Infrastructure, Wanfang, Weipu, China Biology Medicine, Web of Science, PubMed, Cochrane, and Embase. A random-effects model was used to analyze the pooled prevalence of FA for four different assessment methods. A total of 46 eligible articles were included in the narrative synthesis, and 41 articles were ultimately included in the meta-analysis. Overall, the pooled prevalence of self-reported FA, self-reported physician-diagnosed FA, SPT (specific skin prick test)-positive FA, and OFC (open food challenge)-positive FA were 11.5% (95% CI: 9.8–13.5%), 5.3% (95% CI: 4.2–6.5%), 11.6% (95% CI: 9.6–14.1%), and 6.2% (95% CI: 4.4–8.7%), respectively. Subgroup analyses suggested that the prevalence of FA was affected by age, year of data collection, region, and sample size, but not by gender. This meta-analysis indicated that FA is common among Chinese people, with an increasing trend in prevalence during the past two decades. Given the high heterogenicity between these studies, a national survey with a large sample size based on standardized diagnosis is urgently needed to gain a more scientific understanding of the actual situation of food allergy in China.