Per- and polyfluoroalkyl substances (PFAS) are widespread contaminants, but few studies have explored the relationship between PFAS and levels of metabolic syndrome (MetS) in the population. The available evidence of an association is also conflicting. We selected adults and adolescents with complete PFAS data from the National Health and Nutrition Examination Survey conducted between 2003 and 2018. We analyzed the association between PFAS and MetS using multivariate logistic regression models and evaluated potential nonlinear relationships with restricted cubic spline models. Additionally, we employed weighted quantile sum (WQS) regressions to uncover the multiple exposure effects and relative weights of each PFAS. Finally, we conducted a series of sensitivity analyses to test the robustness of our findings. In this population-based study, we analyzed data from a total of 4,973 adults, aged 20–85 years, and 1,381 adolescents, aged 12–19 years. Using fully adjusted multivariate logistic regression models, we found that serum levels of perfluorodecanoate (PFDA) [0.65 (0.50, 0.85)] and total PFAS [0.92 (0.85, 0.99)] were negatively associated with the prevalence of MetS in adults. Similarly, in adolescents, we observed negative correlations between the prevalence of MetS and levels of PFDA [0.55 (0.38, 0.80)], perfluorooctanoic acid (PFOA) [0.62 (0.39, 1.00)], perfluorooctane sulfonic acid (PFOS) [0.59 (0.36, 0.96)], and total PFAS [0.61 (0.37, 0.99)]. Additionally, our study identified statistically significant negative associations between serum levels of PFAS and certain components of MetS, primarily elevated fasting glucose and lower high-density lipoprotein cholesterol. Our study found that PFAS was associated with a lower prevalence of MetS in both adults and adolescents, offering new insights into the relationship between PFAS and metabolic health. Interestingly, however, we observed conflicting findings across the components of MetS. Specifically, we observed that PFAS had a negative correlation with some metrics and a positive correlation with others. These conflicting results point to a complex interplay between PFAS and various metrics of metabolic health.