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Crimean-Congo hemorrhagic fever virus (CCHFV) is a cause of serious hemorrhagic disease in humans. Humans infected with CCHFV develop a non-specific febrile illness and then progress to the hemorrhagic phase where case fatality rates can be as high as 30%. Currently there is lack of vaccines and the recommended antiviral treatment, ribavirin, has inconsistent efficacy in both human and animal studies. In this study we developed a model of CCHFV infection in type I interferon deficient mice using the clinical CCHFV isolate strain Hoti. Mice infected with strain Hoti develop a progressively worsening and ultimately fatal disease. We utilized this model along with our established model using the prototypical CCHFV strain 10200 to evaluate treatment with ribavirin or the antiviral favipiravir. While ribavirin treatment was able to suppress viral loads at early time points it was ultimately unable to prevent development of terminal disease in mice infected with either strain of CCHFV. In contrast, favipiravir showed clinical benefit even when administered late in the clinical progression of CCHF. Interestingly, in a small subset of mice, late-onset of CCHF was observed after favipiravir treatment was stopped and persistence of viral RNA in favipiravir treated survivors was also seen. Nevertheless, favipiravir showed significant clinical benefit against two distinct strains of CCHFV suggesting it may be a potent antiviral for treatment of human CCHFV infections.IFNAR−/− mice infected with CCHFV strain Hoti develop a progressively worsening, ultimately fatal disease.Favipiravir but not ribavirin protects IFNAR−/− mice from lethal CCHFV strain Hoti or strain 10200 infections.Favipiravir treatment can be started late in the clinical progression of CCHFV with clinical benefit.Despite favipiravir treatment, persistence of CCHFV is seen in some surviving mice.