Objective: Frozen section procedure gives a great advantage of fertility preserving in young women with borderline ovarian tumors (BOTs). However diagnostic accuracy of frozen section in BOTs is not as high as the other ovarian lesions. In the present study, we aimed to evaluate the comparison of frozen section results and final pathology results in patients with BOTs. Material and Methods: A total of 97 patients who had BOTs, either on the frozen section or final paraffin section in our clinic between 2007 and 2017 were included in the study. Frozen section and final pathology were compared with medical records of the patients such as age, menstruation, preoperative serum CA-125 and CA 19-9 values, histological diagnosis, subtype, size, localization, and capsule involvement. Results: In BOTs, the diagnostic accuracy of the frozen section was 67%. Frozen section has 74% sensitivity, 40% specificity, 83% positive predictive value and 29% negative predictive value. In the present study, the only factor that affects the accordance between the frozen section and the final paraffin section was the papillarity of the tumor, and it was observed that when the tumor was more papillary, the results had been more compatible. Conclusion: In BOTs, surgical management should be performed with caution depending on the frozen section to avoid overtreatment, especially in young women.