Co-infection with hepatitis C virus (HCV) and Human immunodeficiency virus (HIV) is common in Injecting drug users (IDUs). The aim of this study was the molecular identification of HCV genotypes in IDUs having HC/HIV co-infection in Peshawar. A cohort cross-sectional study was conducted in Nai Zindagi NGO from 2020 to 2022. A sample of 350 IDUs including 309 males, 23 females, 09 children, and 09 transgender were enrolled. Suspected age was 34 years. Screening of HIV and HCV infection was performed through ICT and RT-PCR. For genotype determination, a specific SACACE real-time PCR kit was used. Out of a total of 350 patients, 204 were HCV/HIV co-infected. According to bivariate analysis, there is statistically moderate positive r=522 between viral load and HCV/HIV co-infection (p=0.000). It is concluded that the prevalence of HCV/HIV co-infection was 44.28% in IDUs with the prevalent genotype 3a (51.1%). Viral load of males was higher than females. To overcome the burden of HCV/HIV co-infection large-scale, multicentre, and multistate studies should be conducted across Pakistan and preventive measures should be taken to reduce the use of syringes, razors, tattooing, sex workers, and blood transfusion.