This systematic review and meta-analysis explored HIV prevalence and mortality in children undergoing treatment for severe acute malnutrition (SAM) in sub-Saharan Africa. It included all studies reporting on HIV infection within a sample of children with SAM where HIV status was assessed using a blood test and SAM was defined using the WHO, Gomez, Wellcome or Waterlow definitions. Children from 17 studies were included in the analysis (n=4891), of whom 29.2% were HIV-infected. HIV-infected children were significantly more likely to die than HIV-uninfected children (30.4% vs. 8.4%; P<0.001; relative risk=2.81, 95% CI 2.04-3.87). HIV-negative children treated within community-based therapeutic care (CTC) programmes had lower mortality (4.3%) than those treated within an inpatient nutrition rehabilitation unit (NRU) (15.1%). There was no significant difference in mortality for HIV-infected children with SAM treated in the CTC (30.0%) or NRU (31.3%) settings. HIV prevalence is high in children with SAM in sub-Saharan Africa, and HIV-infected children are at significantly increased risk of mortality. There is an urgent need to integrate HIV testing and treatment into care for children with SAM in regions of high HIV prevalence.