Background Recently, thymectomy using minimally invasive approaches has been increasing with the development of robotic video-assisted thoracoscopic surgery (R-VATS). Although multimodal approach is effective for robot assisted thymectomy, it is necessary to determine the approach (left, right or subxiphoid) associated with the least complications. Methods An electronic retrieval from PubMed, Embase, Web of Science, GreyNet International and The Cochrane Library. The single-arm meta-analysis was performed to compare the rate of complications of right- and left-side approaches by R-VATS. Results A total of 21 studies including 930 patients were identified. The pooled incidence of total complications was 12.2% (confidence interval: 10.0%-14.8%) for all studies. The overall complication rate was 17.3% for the right-side compared with 7.4% for the left side (P < 0.001, odds ratio = 2.484, 1.601-3.852). The pooled incidence of air leak was significantly higher for the right versus left side (5.1% vs. 1.2%, respectively; p = 0.004). The incidence of atrial fibrillation was higher for the right-side compared with the left-side approach (4% vs. 1.2%, respectively; p = 0.004). The open conversion rate was significantly higher for the right versus the left-side (6.5% vs. 2.9%, respectively; p = 0.004). However, there was no significant difference in the pooled incidence of pleural effusion and thoracic duct fistula when comparing the right- and left-side approaches. In subgroup analysis, in the left approach, the incidence of overall complications (28.6% vs. 5.5%, respectively; p = 0.002) and pleural effusion (14.3% vs. 1%, respectively; p = 0.002) was higher for the 'Old Age' group compared with the 'Youth' group; However, In the subgroup analysis of gender, there was no significant difference in the incidence of complications after thymectomy. Conclusion Robotic video-assisted thoracoscopic surgery can be performed on the left- and right-sides; however, complications are minimal with the left-side approach. These data demonstrate that the incidence of overall complications, atrial fibrillation, open conversion ratios, and air leak rate of left-side R-VATS thymectomy are lower than those of right-side. Further subgroup analysis showed that the incidence of postoperative complications was higher in the older group.