Background Medicinal plants are known to perform many pharmacological actions due to their chemical metabolites, which include antiviral effects. Previously, the extract of Ruta angustifolia was shown to have potential anti-hepatitis C virus (HCV) activity without any cytotoxicity, with a 50% inhibitory concentration of 3.0 μg/mL and a 50% cytotoxicity concentration of >100 μg/mL. Furthermore, the combination of medicinal plants and current anti-HCV agents, such as a direct-acting antiviral agent, was shown to potentiate their overall effectiveness. In the course of this study, the ethanolic extract of R. angustifolia was evaluated for its anti-HCV effects; specifically, the mechanism of action on HCV NS3 and NS5A protease was investigated. Methods Analysis of the use of this extract in conjunction with current NS3 inhibitor drugs, simeprevir (SMV) and telaprevir (TVR), was performed. Anti-HCV activity was performed by in vitro culture of hepatocyte cells. The cells were infected and treated with various concentrations of the sample. HCV inhibition was calculated and CompuSyn software analysis was used to determine the synergistic effect of the combination. Results Results demonstrated that R. angustifolia extract inhibited the post-entry step and decreased the protein levels of HCV NS3 and NS5A. The combination of extract and SMV and TVR mediated a synergistic effect. Conclusions These findings suggest that combining R. angustifolia extract with current anti-HCV drugs should be considered when developing alternative and complementary anti-HCV medicines.