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Background/Objectives: Borderline ovarian tumor (BOT) is an ovarian neoplasm of low malignant potential that lacks stromal invasion. The aim of this study was to compare intraoperative frozen section analysis (IFSA) findings with final pathology results in patients diagnosed with BOT on frozen sections and to identify risk factors associated with cancer. Methods: This study included data from patients who underwent surgery for an ovarian mass between 2020 and 2024 and were diagnosed with BOT on IFSA. Demographic, obstetric, and clinical characteristics, as well as frozen section and final pathology findings, were recorded. The CAR, NLR, and PNI scores were calculated. Patients were grouped as premenopausal or postmenopausal and compared. Based on the final pathology report, patients were also classified as having BOT or cancer and compared. Results: A total of 92 patients were included in the study, and 53 (57.6%) were postmenopausal. The prevalence of cancer was significantly higher in the postmenopausal group (p = 0.022). Final pathology revealed cancer in 11 patients (11.9%). Age group > 45 years (OR = 12.50) and serous subtype on IFSA (OR = 10.77) were significant risk factors for cancer detection. Cutoff values for distinguishing carcinoma from BOT were identified for CAR (≥1.75), NLR (≥2.64), and PNI (≤48.64). Conclusions: In this study, the rate of invasive carcinoma on final pathology among patients diagnosed with BOT on IFSA was 11.9%. Age group > 45 years and serous subtype on IFSA were independent risk factors. The cutoff values for CAR, NLR, and PNI may support risk stratification for carcinoma.