Objectives To systematically review the efficacy of polytetrafluoroethylene (PTFE) covered stent grafts vs. bare stent grafts in transjugular intrahepatic portosystemic shunt (TIPS) for portal hypertension. Methods PubMed, EMbase, The Cochrane Library, and ClinicalTrial.gov were searched online to collect randomized controlled trials (RCTs) and cohort studies of PTFE-covered stent grafts vs. bare stent grafts for portal hypertension from inception to Jan 11th, 2017. Two reviewers independently screened literature, extracted data and assessed the risk of bias of included studies. Meta-analysis was then performed by RevMan 5.3 software. Results A total of 4 RCTs and 11 cohort studies involving 2 422 patients (1 070 PTFE-covered stent grafts patients and 1 352 bare stent grafts patients) were included. The results of meta-analysis showed that compared with the bare stent grafts group, the PTFE-covered stent grafts group had higher patency rate of intrahepatic shunt (HR=0.38, 95%CI 0.31 to 0.47, P<0.000 01) and survival rate (HR=0.59, 95%CI 0.44 to 0.79,P=0.000 5), lower postoperative complications rate (including gastrointestinal bleeding and refractory ascites) (HR=0.44, 95%CI 0.33 to 0.58, P<0.000 01) and encephalopathy rate (HR=0.76, 95%CI 0.57 to 0.99,P=0.05). Conclusions Current evidence shows that compared with the bare stent grafts, the PTFE-covered stent grafts could effectively improve patency rate of intrahepatic shunt and survival rate with less postoperative complications rate and encephalopathy rate. Due to limited quality and quantity of the included studies, more high quality studies are required to verify above conclusions.