Limited data exist on the relation between neck circumference (NC) and the risk of developing metabolic syndrome (MS). This study investigated sex-specific associations between NC and the 14-year risk of MS and explored the impact of the FTO rs9939609 polymorphism on these associations. This population-based prospective cohort study involved 2,666 participants (1,301 men and 1,365 women), who were free of MS at baseline (2005-2006). Incident MS cases, defined by the presence of 3 or more criteria regarding blood pressure and blood levels of glucose, triglycerides, and high-density lipoprotein cholesterol, were identified through biennial examinations until 2020. NC measurements taken at baseline and between 2013 and 2014 were analyzed using Cox proportional hazard regression to determine sex-specific associations with MS risk. Controlling for potential confounders such as waist circumference (WC), significant associations were observed in both sexes. Individuals in the highest NC quartile exhibited more than a 2-fold higher MS risk than those in the lowest quartile; with hazard ratios of 2.37 (95% CI, 1.74 to 3.22) for men and 2.65 (95% CI, 1.89 to 3.72) for women (p-value for trend <0.001). No significant interaction was found between the FTO polymorphism and NC. In diagnostic test analyses, NC and WC demonstrated comparable area under the curve values in both sexes. The findings suggest that NC is as effective as WC for predicting the incidence of MS.