There are several types of benign renal diseases, such as urological stones, ureteropelvic junction obstruction, renal vascular disease, and inflammation, which are responsible for nonfunctioning kidneys. Laparoscopic nephrectomy (LN) is the gold standard for treating nonfunctioning kidneys with complications. This study presents the results of our initial experiences with 3D laparoscopic nephrectomy (3D-LN) for benign, nonfunctioning kidneys. From July 2021 to July 2023, 40 consecutive patients who underwent 3D transperitoneal laparoscopic nephrectomy were retrospectively evaluated at the Department of Urology and Department of General Surgery, Hue Central Hospital, Hue, Vietnam. Patient demographics, intraoperative and early postoperative results, postoperative recovery, complications, and three-month follow-up results were recorded. The mean age was 58.35 ± 14.9 years. There were 13 (32.5%) male and 27 (67.5%) female patients. Flank pain was the main reason for hospitalization in 33 cases (82.5%); the common cause of a nonfunctioning kidney was urological stones (62.5%). Twenty-three out of 40 patients underwent a left nephrectomy. The average operative time was 92.57 ± 28.69 minutes. A statistically significant difference in surgery time was found between the group with no adhesion and the group with mild adhesion, as well as between the first 19 patients and the last 18 patients (p <0.05). The mean blood loss was 51.62 ± 24.35 ml. Three cases were converted to open surgery due to severe adhesions. The postoperative complications rate was 8.1%. The average length of the postoperative hospital stay was 7.89 ± 3.59 days. Three-dimensional laparoscopic nephrectomy is a safe and effective method that increases depth perception and spatial orientation for surgeons and can compensate for the remaining shortcomings of traditional 2D systems.