Health care workers (HCWs) in eastern Africa experience high levels of burnout and depression, and this may be exacerbated during the COVID-19 pandemic due to anxiety and increased work pressure. We assessed the prevalence of burnout, depression and associated factors among Malawian HCWs who provided HIV care during the COVID-19 pandemic. From April-May 2021, between the second and third COVID-19 waves in Malawi, we randomly selected HCWs from 32 purposively selected PEPFAR/USAID-supported health facilities for a cross-sectional survey. We screened for depression using the World Health Organization Self Report Questionnaire (positive screen: score≥8) and for burnout using the Maslach Burnout Inventory tool, (positive screen: moderate-high Emotional Exhaustion and/or moderate-high Depersonalization, and/or low-moderate Personal Accomplishment scores). Logistic regression models were used to evaluate factors associated with depression and burnout. We enrolled 435 HCWs, median age 32 years (IQR 28-38), 54% male, 34% were clinical cadres and 66% lay cadres. Of those surveyed, 28% screened positive for depression, 29% for burnout and 13% for both. In analyses that controlled for age, district, and residence (rural/urban), we found that screening positive for depression was associated with expecting to be infected with COVID-19 in the next 12 months (aOR 2.7, 95%CI 1.3-5.5), and previously having a COVID-19 infection (aOR 2.58, 95CI 1.4-5.0). Screening positive for burnout was associated with being in the clinical cadre (aOR 1.86; 95% CI: 1.2-3.0) and having a positive depression screen (aOR 3.2; 95% CI: 1.9-5.4). Reports of symptoms consistent with burnout and depression were common among Malawian HCWs providing HIV care but prevalence was not higher than in surveys before the COVID-19 pandemic. Regular screening for burnout and depression should be encouraged, given the potential for adverse HCW health outcomes and reduced work performance. Feasible interventions for burnout and depression among HCWs in our setting need to be introduced urgently.