The study was undertaken to investigate the efficacy and safety of Saccharomyces boulardii combined with proton pump inhibitor (PPI)-based triple therapy for Helicobacter pylori related peptic ulcer. One hundred patients with H. pylori infection were randomized in two groups: intervention and control group. Both groups were treated with the standard triple eradication therapy (omeprazole, amoxicillin and clarithromycin). The effective rate of the improvement in the treatment group was 96.0%, and was significantly higher than the control group (62.0%) (x 2 = 6.899, P < 0.01). The pH of the two groups was also elevated after the treatment (P < 0.05, P < 0.05); the positive culture rate of bacteria increased obviously and there was significant difference between the two groups (P < 0.05). The eradication rate of H. pylori in the treatment group was 84.4% and was significantly higher than the control group (64.4%) (x 2 = 5.848, P < 0.01). In addition, the rate of recurrence in the treatment group was 10.0%, while in the control group it was 26.0% after treated for one year (x 2 = 11.584, P < 0.01). There was significant difference in the rate of adverse events between the two groups (15.6 and 57.8% of the treatment group and control group, respectively; x 2 = 18.936, P < 0.01). Therefore, S. boulardii with PPI-based triple therapy for peptic ulcer is effective with a low recurrence rate and can reduce the incidence of adverse events.