Background: Helicobacter pylori infection is highly prevalent worldwide and affects more than half of the world's population. A variety of treatment regimens to eliminate H. pylori infection have been evaluated, but choosing the best treatment method that results in the most eradication at the lowest cost is one of the challenges facing physicians. Therefore, the present study aimed at analyzing the cost-effectiveness of using different methods to treat H. pylori in southern Iran. Methods: This study was a cost-effectiveness analysis conducted on 132 patients with H. pylori who referred to Shahid Motahari Clinic in Shiraz. The study was carried out in 2020 to evaluate two drug treatment strategies, including antibiotics (pantoprazole 40 mg, Bismuth subcitrate 108 mg, tetracycline 500 mg, and metronidazole 200 and 400 mg) and plants (Supermint Barij soft capsules 20 mg, Alium S garlic tablets 400 mg, and Green Teadin (green tea) tablets 500 mg). The patients were randomly divided into two groups, 64 of whom received an antibiotic regimen and 68 patients given a plant regimen. The success rate of clinical trials in each treatment method was determined as the clinical outcome. This study was conducted from a community perspective and therefore, direct and indirect costs were included. A data collection form was also used to collect the cost and effectiveness data. In addition, a one-way sensitivity analysis was performed to measure the robustness of the results. The data were analyzed using TreeAge Pro 2011 and Excel 2016 software. Results: The results showed that antibiotic treatment was cheaper and more effective than plant treatment and was the dominant strategy. The mean costs in the antibiotics and plant groups were $446.14 and $477.81, respectively, and the effectiveness was 0.625% and 0.382%. In addition, the one-way sensitivity analysis confirmed the robustness of the study results. Conclusion: The results showed that the use of antibiotics was a cost-effective and dominant strategy compared to plant treatment and could be suggested as a better alternative to a wide range of patients with Helicobacter pylori infection.