Introduction: Treatment of Helicobacter pylori has various side effects like antibiotic resistance. The purpose of this study was to evaluate the effects of cinnamon extract on complications of treatment and eradication of H. pylori in infected people. Methods: In this randomized clinical trial, a total of 98 eligible healthy and H. pylori-infected patients approved by esophageal endoscopy were selected. The cinnamon group received multi-drug treatment including clarithromycin, amoxicillin and pantoprazole as well as a cinnamon extract capsule. The control group received multi-drug treatment and a 40 mg starch capsule. In order to analyze the cinnamon extract efficacy, the urea breath test (UBT) was performed 3 months after the start of treatment. Clinical symptoms were evaluated by a questionnaire at the beginning (day of 0), 7 days and 14 days after starting treatment. Results: The clinical symptoms such as nausea, vomiting, diarrhea, constipation, blurred vision, headache, metallic flavor, epigastric pain, burp, and appetite were significantly reduced in the cinnamon group (P < 0.05). The odds ratio exhibited a higher eradication rate of H. pylori in the cinnamon group (73.47% in the cinnamon group compared to 53.06% in the control group) (P = 0.036). Conclusion: Cinnamon as assisted therapy is able to alleviate the disease and reduce the complications of H. pylori treatment.