The effect of highly active antiretroviral therapy (HAART) on hepatitis C virus (HCV) infection remains uncertain. This report describes the case of a man with hemophilia with HIV-HCV coinfection with persistent disappearance of HCV RNA after changing the HAART regimen. He had been treated with zidovudine, lamivudine, and indinavir for initial HAART and the HIV RNA level had been undetectable for more than 8 years. He had suffered from chronic active hepatitis. The HAART regimen was changed to emtricitabine/tenofovir, atazanavir, and ritonavir because the patient preferred a once daily regimen. The HCV RNA level fell immediately and thereafter became undetectable by quantitative and qualitative assay at 5 and 7 months after the change of the HAART regimen, respectively. In contrast to other reported cases, he experienced neither increase of CD4+ T cells count nor ALT flare-ups before HCV RNA clearance. The HCV RNA disappearance in this case may be due to the direct effect of HAART against HCV rather than restoration of cellular immunity to HCV.