Polycystic ovary syndrome (PCOS) is a heterogeneous disorder and associated with metabolic disturbances such as insulin resistance (IR) and obesity which are risk factors for cardiovascular diseases. Many studies have shown that waist circumference (WC) representing abdominal obesity is an important risk factor for IR. However, there were few studies whether WC were associated with IR in young women with PCOS. We aimed to evaluate the role of WC in IR among young Korean women with PCOS. We enrolled age- and body mass index-matched women with PCOS (n = 100) and controls (n = 100). WC was measured and the 75-gram oral glucose tolerance test (OGTT) was performed. Insulin sensitivity was assessed by the Stumvoll index which was calculated from an OGTT. Multiple linear regression analysis was performed to evaluate the association between WC and IR. WC, fasting glucose, post-load 2-hour glucose, fasting insulin, and post-load 2-hour insulin did not differ between women with PCOS and controls. Women with PCOS had lower values of the Stumvoll index than the controls. In correlation analysis, WC was negatively correlated with the Stumvoll index in women with PCOS, however not in controls. In multiple regression analysis, WC was negatively associated with the Stumvoll index even after adjustment for age, total cholesterol, and total testosterone in women with PCOS. In young Korean women with PCOS, WC was negatively associated with insulin sensitivity independent of hyperandrogenemia. Simply measuring of WC could be used to screen the high risk group having IR in young women with PCOS.