(1) Background: we conducted this study to evaluate the effect of Kono-S anastomosis on postoperative morbidity after bowel resection for Crohn’s disease. (2) Methods: This study adhered to the PRISMA guidelines and the Cochrane Handbook for Systematic Reviews of Interventions. The primary endpoint was the overall complications rate. Secondary outcomes included specific complications analyses, disease recurrence and efficiency endpoints. A systematic literature screening was performed in major electronic scholar databases (Medline, Scopus, Web of Science), from inception to 17 January 2024. Both Random (RE) and Fixed Effects (FE) models were estimated; the reported analysis was based on the Cochran Q test results. (3) Results: Overall, eight studies and 913 patients were included in this meta-analysis. Pooled analyses confirmed that Kono-S was not superior in terms of overall morbidity (OR: 0.69 [0.42, 1.15], p = 0.16). Kono-S displayed a reduced risk for anastomotic leakage (OR: 0.34 [0.16, 0.71], p = 0.004) and reoperation (OR: 0.12 [0.05, 0.27], p < 0.001), and a shortened length of hospital stay (WMD: −0.54 [−0.73, −0.34], p < 0.001). On the contrary, Kono-S results in higher rates of postoperative SSIs (OR: 1.85 [1.02, 3.35], p = 0.04). (4) Conclusions: This study confirms a comparable morbidity, but a lower risk of anastomotic leak and reoperation of Kono-S over conventional anastomoses. Further high quality studies are required to validate these findings.