Background: The COVID-19 pandemic has resulted in a significant decrease in the number of surgical procedures performed. Therefore, it is important to use surgical methods that carry the lowest possible risk of virus transmission between the patient and the operating theater staff. Aim: Safety evaluation of three-dimensional (3D) versus two-dimensional (2D) laparoscopic hysterectomy during the COVID-19 pandemic. Methods: 44 patients were assigned to a prospective case-control study. They were divided either to 3D (n = 22) or 2D laparoscopic hysterectomy (n = 22). Fourteen laparoscopic supracervical hysterectomies (LASH) and eight total laparoscopic hysterectomies (TLH) were performed in every group. The demographic data, operating time, change in patients’ hemoglobin level and other surgical outcomes were evaluated. Results: 3D laparoscopy was associated with a significantly shorter operating time than 2D. (3D vs. 2D LASH 70 ± 23 min vs. 90 ± 20 min, p = 0.0086; 3D vs. 2D TLH 72 ± 9 min vs. 85 ± 9 min, p = 0.0089). The 3D and 2D groups were not significantly different in terms of change in serum hemoglobin level and other surgical outcomes. Conclusions: Due to a shorter operating time, 3D laparoscopic hysterectomy seems to be a safer method both for both the surgeon and the patient. Regarding terms of possible virus transmission, it may be particularly considered the first-choice method during the COVID-19 pandemic.