Background: Ectopic pregnancy (EP) is the most common cause of death in the first trimester of pregnancy. Methotrexate (MTX) is an acceptable treatment in the cases with the lack of tube rupture or no important one, which has reduced surgical treatment. Despite numerous studies, there is still no consensus about medications. The present study is aimed to evaluate the single- and multiple-dose of MTX among these patients. Materials and Methods: This clinical trial study was done on 108 EP patients who were selected for the systemic MTX treatment and divided into two groups. For the single-dose group, MTX was administered once and β human chorionic gonadotropin (βHCG) levels were measured first and then on days 4 and 7. In the multi-dose group, 1 mg/kg MTX was injected on days 1, 3, 5, and 7. In both groups, MTX was prescribed following these days if βHCG was not reduced. In the two groups, βHCG levels were assessed after 1 week. The success rate of treatment and complications were followed up and recorded up to 6 weeks after treatment. Results: The success rate in the single-dose and multiple-dose MTX group was 47% and 51%. The MTX level in the single dose group decreased from 2532 ± 1154 mIU/mL to 1341 ± 553 mIU/mL and in the multiple dose group from 2671 ± 2685 mIU/mL to 1313 ± 605 mIU/mL (P < 0.05). Although a significant decrease was observed in each of the two groups over time, no significant difference was found between the two groups (P > 0.05). Conclusion: Single and multi-dose regimen did not show a significant difference in terms of the success of treatment. Therefore, given that the lower dose of the drug associated with lower the risk of complications, it is safe to choose the single-dose regimen.