Patient-initiated repackaging of antiretroviral therapy (ART) refers to removal of ART medications from their original manufacturer’s containers, and putting them into alternative containers. This behavior may be triggered by stigma associated with HIV infection, and may impact patient outcomes. We assessed association between patient initiated repackaging of ART and failure to achieve viral suppression (FVS) in a sample of 450 HIV-infected adults (≥8 years) on first line ART for ≥6 months. FVS was defined as a plasma HIV RNA level ≥400 copies/mL. A total of 197 (43.7%) patients reported repackaging their ART medications. One hundred ninety-one patients (42.4%) failed to suppress and FVS was associated with medication repackaging [adjusted odds ratio (aOR), 2.2; 95% CI 1.4–3.3.] Adherence to ART was also associated with FVS (aOR; 0.4; 95% CI 0.2–0.6.). Benefits of retaining drugs in their original packaging along with adherence to ART should be emphasized to reduce the risk of FVS.