Background: Laparoscopy is widely used in the urological field. This systematic review and a meta-analysis were conducted to assess the clinical and surgical efficacy of the three-dimensional (3D) laparoscopic system in comparison with two-dimensional (2D) laparoscopy for treatment of different urological conditions. Methods: Following guidelines of Preferred Reporting Items for Systematic Reviews and Meta-Analyses, a systematic literature search in Web of Science, PubMed, Cochrane Library, and EMBase was carried out to identify relevant studies published up to May 2018. Articles published in the English language of both randomized and observational studies comparing 3D and 2D laparoscopic systems in urological surgeries were included. Level of evidence and quality assessments of all included studies were conducted. Interested data were extracted for comparison and meta-analysis. Results: Our literature search generated 17 studies comparing 3D and 2D laparoscopic systems in different urological surgeries. Of these, 13 studies containing 548 and 449 patients operated on with 2D and 3D laparoscopic systems, respectively, were included for meta-analysis. These 13 studies were divided into three groups according to surgical type. Group 1: Partial nephrectomy (PN); operative time (p=0.19), estimated blood loss (EBL) (p=0.51), dissecting time (p=0.58), and suturing time (p=0.28) were not statistically significant between 2D and 3D laparoscopic systems. However, warm ischemia time during PN was significantly shorter during 3D laparoscopy (p<0.00001). Group 2: Pyeloplasty; this procedure showed no significant difference between the two systems. Group 3: Radical prostatectomy (RP); shorter operative time (p<0.0001) and lower EBL (p=0.001) were associated with the 3D laparoscopic system. Conclusion: Three-dimensional laparoscopy mainly improves the depth of perception, leading to better visibility, which is important for some complex urological surgeries such as PN, pyeloplasty, and RP. Based on our findings, 3D laparoscopy seems to provide better clinical and surgical outcomes in some urological procedures compared with conventional 2D laparoscopy.