Background: We aimed to evaluate the association between thyroid hormone (free thyroxine, free T4) level and lipid profiles in nationally representative data. Methods: This study was based on cross-sectional survey data from the sixth Korea National Health and Nutrition Examination Survey IV. After exclusion of subjects with a history of thyroid disease or abnormal thyroid function test and those on medication for dyslipidemia and/or cardiovascular disease, a total of 3548 subjects were included in the study. Results: There was a significant decrease in serum triglyceride levels and increase in serum high-density lipoprotein (HDL) cholesterol levels with high free T4 quartiles after adjustment for confounding factors (p for trend = 0.001 and p for trend = 0.014, respectively). Risk of hypertriglyceridemia was significantly decreased (odds ratio of 0.72 (95% confidential interval 0.53–0.98)) in the highest free T4 quartile compared to the lowest free T4 quartile, p = 0.044). Conclusions: Serum free T4 levels within normal range negatively correlated with serum triglyceride level and positively correlated with HDL-cholesterol level. Therefore, a close surveillance in terms of lipid profiles could be considered in subjects with low normal serum free T4 levels.