Purpose Borderline ovarian tumors (BOTs) are more common in young women of reproductive age, and exhibit a better prognosis than malignant ovarian tumors (MOTs). Fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (PET/CT) were compared in their ability to differentiate BOTs from stage I MOTs. Methods Among 173 patients who had preoperative FDG PET/CT due to ovarian neoplasms between November 2006 and March 2009, there were 13 patients with BOTs or stage I MOTs. For differential diagnosis of the two tumors, cancer antigen-125 (CA-125) level, the longest diameter of tumors, metabolic indices including maximum standardized uptake value (SUV max ), and volumetric indices including metabolic tumor volume (MTV) were compared, respectively. Results The BOT group (n=7) was comprised of five mucinous and two serous tumors, and the MOT group (n=6) was comprised of three endometrioid, two clear cell and one mucinous tumors. Among the comparisons between two groups, SUV max of the BOT group was significantly lower than that of the MOT group (2.9±1.5 vs. 6.6±2.9, p=0. 0223); otherwise, no significant difference was found in age, CA-125, diameter, or MTV. By receiver-operating characteristic curve analysis, SUV max of 3.7 was the best cutoff value to differentiate BOTs from stage I MOTs, with a sensitivity of 83.3 % and specificity of 85.7, and the area under curve of 0.893 (p=0.0001, 95 % CI: 0.601∼0.993). Conclusions We demonstrated that SUV max could distinguish BOTs from stage I MOTs, with a high sensitivity and specificity. Metabolic indices determined by FDG PET/CT were more suitable than volumetric indices for differential diagnosis of the two tumors.