BackgroundEthiopia is one of the nation’s most severely impacted by HIV, with an estimated 700,000 people living with HIV/AIDS. Hence, many health facilities were providing second-line antiretroviral therapy, however little was known about viral load suppression among second-line users. This study aimed to assess the proportion of viral load suppression and associated factors among HIV-infected patients on second-line antiretroviral therapy at public health facilities of west Guji, Guji and Borena zones, Southern Ethiopia.MethodsA facility-based cross-sectional study was conducted among 256 HIV-infected patients on second-line antiretroviral therapy from January 1, 2019, to December 30, 2022, by using census after obtaining ethical clearance from Bule Hora University ethical review committee. Data were extracted using a structured, pre-tested checklist, entered into the EPI data version 3.1.0, and exported to SPSS version 25 for analysis. The proportion of viral load suppression was determined. A binary logistic regression model was fitted to identify factors associated with viral load suppression. Statistical significance was declared at a 95% confidence interval (CI) with a P-value <0.05.ResultsThis study revealed that the proportion of viral load suppression among HIV-infected patients on second-line antiretroviral therapy was 73.8% (95% CI, 68.0–79.1). Those who missed the second-line antiretroviral regimen [AOR = 0.315, 95% CI (0.162–0.612)], a baseline viral load count of <10,000 copies/mm3 [AOR = 2.291, 95% CI (1.216-4.316)], and a baseline body mass index of ≥18.5 kg/m2 [AOR = 2.438, 95% CI (1.098–5.414)] were significantly associated with viral load suppression.ConclusionsThe proportion of patients with viral load suppression fell below the WHO’s and national level. Viral load suppression was significantly influenced by missed second-line antiretroviral doses, a baseline viral load count of <10,000 copies/ml, and a baseline body mass index of ≥18.5 kg/m2. Hence interventions targeting counseling to patients that missed their antiretroviral therapy, keeping patient’s viral load to be less than 10,000 copies/ml through adequate adherence counseling among second-line antiretroviral therapy were recommended.