Objective To evaluate the clinical effectiveness of helicobacter pylori (HP) eradication in treating functional dyspepsia (FD) patients with HP infection. Methods The randomized controlled trials (RCTs) about HP eradication vs. general treatment for FD patients published by April, 2012 were searched in the following databases: CBM, CNKI, WanFang Data, PubMed, Ovid, EMbase and The Cochrane Library (Issue 1, 2012). According to the inclusion and exclusion criteria, two reviewers independently screened studies, extracted data, and evaluated the methodological quality. Then the meta-analysis was conducted using RevMan 5.1 software. Results The total 14 RCTs were included. Among all 2 665 patients involved in, 1 339 were in the treatment group, while the other 1 326 were in the control group. The results of meta-analysis showed that HP eradication was superior to general treatment for FD patients in clinical effects (RR=3.90, 95%CI 3.08 to 4.94, Plt;0.000 01), symptomatic score (WMD=−1.68, 95%CI −1.88 to −1.47, Plt;0.000 01), and improvement of upper abdominal pain (RR=2.84, 95%CI 2.02 to 3.99, Plt;0.000 01). Conclusion With obviously clinical effects, HP eradication can decrease the symptomatic score of dyspepsia, and especially improve upper abdominal pain. For the quality and quantity limitations of the included studies, more well-designed and double blind RCTs are required to further prove this conclusion.