Aims: To determine the association between free triiodothyronine (FT3), free thyroxine (FT4) and free-triiodothyronine-to-free-thyroxine ratio (FT3/FT4) levels and Metabolic Syndrome (MetS). Materials and methods: We carried out an analytical cross-sectional study in euthyroid adults of both sexes, who attended the outpatient service of a private clinic in Lima-Peru during the 2014–2016 period. Participants were divided into tertiles (low, intermediate and high) according to their FT3, FT4, and FT3/FT4 ratio values. MetS was defined when three or more metabolic criteria were met by the participants. ROC curves were constructed, and Youden's Index were used to identify the optimal cut-points of each thyroid marker. We elaborated crude/adjusted Poisson regression models to evaluate the association between the thyroid markers and the presence of MetS. The reported association measure was the prevalence ratio (PR) with their respective 95% confidence intervals (95% CI). Results: We analyzed 245 participants, the average age was 38.5 ± 10.3 years, 29.8% were males, and the prevalence of MetS was 31%. In the adjusted Poisson regression models, the prevalence of MetS was higher among the high FT3 tertile compared to the low tertile (aPR = 2.01; 95% CI: 1.22–3.34). The prevalence of MetS was higher among the intermediate FT3/FT4 ratio tertile and the high FT3/FT4 ratio tertile compared to the low tertile, (aPR = 1.78; 95% CI: 1.02–3.10) and (aPR = 2.80; 95% CI: 1.67–4.72); respectively. The highest areas under the curve (AUC) were found for FT3 and FT3/FT4 ratio with areas of 0.654 (95% CI: 0.58–0.73) and 0.649 (95% CI: 0.57–0.72); respectively. Conclusion: Elevated levels of FT3 and FT3/FT4 ratio were associated with MetS in a euthyroid population.