Shared transmission routes of HCV and HIV mean parenteral HIV/HCV coinfection still occurs, often in resource-limited settings. The extent to which coinfection and treatment impact on morbidity and mortality in HIV/HCV coinfected children remains unknown thus optimal management and treatment is difficult to achieve. Using data from a unique, large, prospective cohort of parenterally HIV/HCV coinfected children in Libya we determine the immunological, virological and clinical profiles of HIV/HCV coinfected children documenting the natural and treated history of parenterally acquired coinfection for the first time in such a large group. 160 parenterally HIV/HCV coinfected children were analysed. Thirty-three (21%) received antiretroviral treatment (ART) for HIV disease during follow-up. In children receiving ART, HIV RNA viral load decreased in two-thirds 6-12 months after initiation. 85% (17/20) experienced a positive immunological response to ART with a median increase in CD4 cell count z-score of 131%. Half had progressed to moderate or severe immunosuppression and/or moderate or severe clinical symptoms three years after infection. In those who progressed during follow-up, 85% had done so within three years of infection. Children progressing to moderate or severe immunosuppression and/or clinical symptoms were significantly more likely to be receiving ART. This novel investigation of the natural and treated history of parenterally HIV/HCV coinfected children in a large prospectively followed group demonstrates minimal clinical symptoms and immunosuppression to date, despite low prevalence of treatment, and a response to ART similar to vertically HIV-only infected children.