Aim: To investigate the factors related to the effect of eradication therapy with vonoprazan for Helicobacter pylori (H. pylori). Methods: We retrospectively reviewed medical records of H. pylori-positive patients who received first-line (40 mg vonoprazan/60 mg lansoprazole or 20 mg rabeprazole, 1500 mg amoxicillin, 400 mg clarithromycin, all 2/day for 7 days) (n = 4118). H. pylori eradication was assessed by the 13 C-urea breath test with success defined as a result of < 2.5‰. Using propensity score matching, successful eradication rates were compared between two groups: those receiving vonoprazan and those receiving a proton pump inhibitor. Related factors and adverse events were investigated. Results: Successful first-line eradication rates according to ITT analysis and PP analysis, respectively, were 79.8% and 91.4% for VPZ therapy. Eradication rates using propensity matched patients (n = 1053) who received first-line vonoprazan therapy were higher than in those using proton pump inhibitor (PPI) therapy (92.1% vs. 79.7% in per-protocol analysis, p < 0.0001). Multivariate analysis confirmed that gastric mucosal atrophy was associated with treatment success. Conclusions: Low-dose clarithromycin triple therapy for first-line H. pylori eradication therapy using vonoprazan was more effective than standard triple therapy with proton pump inhibitor. Gastric mucosal atrophy was associated with treatment success.