Background: Given that borderline ovarian tumors (BOTs) are usually found in young, fertile women without a history of childbirth, fertility preservation should be considered in the treatment plan. This retrospective study aimed to evaluate the safety of ovarian cystectomy in patients with BOTs. Methods: Patients with BOTs treated between August 2007 and August 2016 at our institution were divided into two groups according to the type of surgery: the cystectomy group and the oophorectomy group with or without salpingectomy, and differences in surgical outcomes were compared. The cumulative disease recurrence was also compared using Kaplan–Meier curves. Results: Of the 162 patients enrolled, 128 (79.0%) underwent an oophorectomy with or without salpingectomy and 34 (21.0%) underwent an ovarian cystectomy. The patients in the cystectomy group were younger than those in the oophorectomy group (29.2 years vs. 46.5 years, p 0.001), and the proportion of patients who underwent minimally invasive surgery was higher in the cystectomy group than in the oophorectomy group (88.2% vs. 46.9%, p 0.001). During the mean follow-up period of 44 months, six patients (3.70%) developed disease recurrence (five [3.9%] and one [2.9%] in the oophorectomy and cystectomy groups, respectively). The two-year disease-free survival rate was 97.1% and 97.6% in the cystectomy and oophorectomy groups, respectively, and did not differ between the groups (p = 0.818). Discussion: Ovarian cystectomy can be considered a safe and effective option for young women with BOTs who wish to preserve their fertility.