Limited evidence on hepatitis A seroprevalence among HIV-exposed uninfected (HEU) children compared to their HIV infected (HIV) and unexposed uninfected (HUU) counterparts compromises rational vaccine decision-making. This study comprised of a retrospective health facility-based population of children aged 1 month – 12 years. Archival sera were tested for markers of acute (anti-HAV IgM) or past (total anti-HAV) HAV infection. Subgroup analysis was conducted based on HIV exposure or infection status. Of 513 participants, 54% (277) were male and the median age was 10 (IQR: 4 – 25) months. The median maternal age was 29 (IQR: 25 – 34) years. An anti-HAV seropositivity of 95.1% (117/122 [95% CI 90.2-98.4]) was found among those ≤6 months of age, indicative of the rate of transplacental antibody transfer. Among 1–12-year-olds, hepatitis A seroprevalence was 19.3% (37/192 [95% CI 14.1-25.7]), while 1.1% (2/188 [95% CI 0.12-2.76]) had evidence of acute infection. Compared to HIV-exposed subgroups (HIV=60%, 6/10 [95% CI 27.4-86.3] and HEU=45%, 9/20 [95% CI 23.8-68]), hepatitis A seroprevalence among HUU children was low (29.2%, 47/161 [95% CI 22.4-37.0]). Natural immunity among HIV -exposed and -unexposed children in South Africa is insufficient to protect against severe liver complications associated with HAV infection later in adulthood.