Background A meta-analysis was conducted in order to provide an up-to-date comparison of pancreatogastrostomy (PG) and pancreatojejunostomy (PJ), after pancreatoduodenectomy (PD), in terms of clinically significant postoperative pancreatic fistula (POPF) and other postoperative complications. Methods This meta-analysis was conducted according to the PRISMA guidelines and the Cochrane Handbook for Systematic Reviews of Interventions. A systematic literature search in MEDLINE and Cochrane Central Register of Controlled Clinical Trials was performed. Fixed Effects or Random Effects model was used, based on the Cochran Q test. Results In total, 10 studies (1629 patients) were included. There was no statistical significance between PG and PJ regarding the rate of clinically significant POPF (OR: 0.70, 95%CI: 0.46–1.06). PG was associated with a higher rate of postpancreatoduodenectomy haemorrhage (PPH) (OR: 1.52, 95%CI: 1.08–2.14). There was no difference between the two techniques in terms of clinically significant PPH (OR: 1.35, 95%CI: 0.95–1.93) and clinically significant postoperative delayed gastric emptying (DGE) (OR: 0.98, 95%CI: 0.59–1.63). Discussion There is no difference between the two anastomotic techniques regarding the rate of clinically significant POPF. Given several limitations, more large scale high quality RCTs are required.