Medical resources are limited for hepatitis C virus (HCV) elimination in rural indigenous areas of Taiwan. This study aimed to investigate liver disease risk and conduct a HCV elimination program in two rural indigenous townships. A program of village-by-village screening tests was conducted including hepatitis B virus surface antigen (HBsAg), antibody to HCV (anti-HCV) and gamma-glutamyl transferase (GGT), linking to outreach hepatology care at two indigenous townships (Laiyi and Mudan). Adult residents were invited to join this program. One hepatology specialist assessed liver disease risk, provided HCV treatment counselling and initiated direct acting antivirals (DAA) at an outreach hepatology clinic in primary health centers. A total of 3503 residents attended this program with a screening coverage of 73.5%. The prevalence of HBsAg, anti-HCV, and high GGT level was 8.2%, 10.0% and 19.5%, respectively. Laiyi had significantly higher prevalence of anti-HCV than Mudan. While males had significantly higher prevalence of HBsAg and high GGT in both townships, females in Laiyi had higher anti-HCV prevalence. HBsAg and high GGT prevalence peaked at 40–59 years of age and anti-HCV prevalence increased significantly with age. Two hundred and sixty-three residents visited the outreach hepatology clinic for HCV treatment evaluation, with 121 (46%) residents having active HCV, while 116 received DAA, with 111 (95.7%) achieving HCV elimination. For rural indigenous townships in southern Taiwan, HCV infection and alcohol consumption were two major liver disease risks. While HCV infection was predominant in old females, chronic hepatitis B virus infection and habitual alcohol consumptions predominated in middle-aged males. HCV elimination was achieved by the village-by-village screening model and linked to outreach hepatology care.