The prevalence of patients co-infected with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) is higher in Taiwan than in Western countries. This study aimed to analyze the frequency and risk factors for highly active antiretroviral therapy (HAART)-related liver toxicity in patients co-infected with HIV and HCV with advanced liver fibrosis in Taiwan.This retrospective cohort study included 228 HAART-experienced and HAART-naïve patients who were co-infected with HIV and HCV from January 2013 to December 2013 in Taiwan. Transaminase elevation (TE) was defined by grades. Fibrosis 4 score and aspartate-to-platelet ratio index were used to evaluate liver fibrosis. Cox proportional hazard regression model was used to analyze the risk factors for time to TE events.A total of 228 patients were included. Only two episodes (1.28%) of high-grade TE were observed. The overall prevalence rate of TE was 16%, and the incidence was 1.38 cases/100 patient-months. Two predictive factors of TE were the initiation of HAART during the study period and CD4 cell count less than 350 cells/mm3. Subgroup analysis showed that HAART improved liver fibrosis status in patients who had advanced liver fibrosis at baseline (p = 0.033).The frequency of HAART-related TE in HIV and HCV co-infected patients in Taiwan was much lower than that observed in previous studies. Pre-existing advanced liver fibrosis had no influence on the frequency of TE. The use of HAART showed benefits on liver fibrosis progression in patients with underlying advanced liver fibrosis.