Concerns are often raised regarding potentially adverse effects of antiretroviral therapy (ART) on health-related quality of life (HRQoL), but there is limited longitudinal data to prove this. Building on our prior investigation, we examined the impact of ART on HRQoL among HIV-infected South African women with extensive follow-up in the CAPRISA 002 Acute Infection Cohort Study. Overall HRQoL and five sub-domains [physical well-being (PWB), emotional well-being (EWB), functional and global well-being (FGWB), social well-being (SWB) and cognitive functioning (CF)] were assessed using the Functional Assessment of HIV Infection (FAHI) instrument. Our analyses comparing FAHI scores between pre-ART (established infection) and ART phases using paired Wilcoxon signed-rank tests and adjusted mixed-effects regression models revealed improvements on ART in overall HRQoL, and in PWB, EWB, and SWB, but not in FGWB and CF. No long-term adverse impact of ART on HRQoL was detected, providing additional non-biomedical support to early treatment strategies.