The study aim was to assess whether hepatitis C virus (HCV) was associated with painful symptoms among patients with HIV. Using data from a prospective cohort of HIV-infected adults with alcohol problems, we assessed the effects of HCV on pain that interfered with daily living and painful symptoms (muscle/joint pain, headache and peripheral neuropathy). Exploratory analyses assessed whether depressive symptoms and inflammatory cytokines mediated the relationship between HCV and pain. HCV-infected participants (n = 200) had higher odds of pain that interfered with daily living over time (adjusted odds ratio [AOR] 1.43; 95% CI: 1.02-2.01; p = 0.04) compared to those not infected with HCV. HIV/HCV co-infected participants had higher odds of muscle or joint pain (AOR 1.45; 95% CI: 1.06-1.97; p = 0.02) and headache (AOR 1.57; 95% CI: 1.18-2.07; p<0.01). The association between HCV and peripheral neuropathy did not reach statistical significance (AOR 1.33; 95% CI: 0.96-1.85; p = 0.09). Depressive symptoms and inflammatory cytokines did not appear to mediate the relationship between HCV and pain. Adults with HIV who are also co-infected with HCV are more likely to experience pain that interfered with daily living, muscle or joint pain, and headaches compared to those not co-infected. Research is needed to explore the association between HCV infection and pain, and to determine whether HCV treatment is an effective intervention.