Background: branched-chain fatty acids (BCFAs) have recently emerged as a group of functional fatty acids that are widely distributed in various foodstuffs, including dairy products, ruminant meat products, and fermented foods. Several studies have investigated the differences in the levels of BCFAs among individuals with varying risks of metabolic syndrome (MetS). In this study, we conducted a meta-analysis to explore the relationship between BCFAs and MetS, and to assess the feasibility of BCFAs as potential biomarkers for diagnosing MetS. Methods: in accordance with the PRISMA guidelines, we conducted a systematic literature search on PubMed, Embase, and the Cochrane Library up to March 2023. Both longitudinal and cross-sectional studies were included. The quality of the longitudinal and cross-sectional studies was evaluated using the Newcastle-Ottawa Scale (NOS) and the Agency for Healthcare Research and Quality (AHRQ) criteria, respectively. Heterogeneity detection and sensitivity analysis of the included research literature were carried out using R 4.2.1 software with a random-effects model. Results: Our meta-analysis included 685 participants and revealed a significant negative correlation between the endogenous BCFAs (serum BCFAs and adipose tissue BCFAs) and the risk of developing MetS, with lower BCFA levels found in individuals at a high risk of MetS (WMD: -0.11%, 95% CI: [-0.12, -0.09] %, P < 0.0001). However, there was no difference in fecal BCFAs among different MetS risk groups (SMD: -0.36, 95% CI: [-1.32, 0.61], P = 0.4686). Conclusion: our study provides insights into the relationship between BCFAs and the risk of developing MetS, and lays the groundwork for the development of novel biomarkers for diagnosing MetS in the future.