Using a systematic review method, the prevalence of anaemia, iron deficiency (ID), and iron deficiency anaemia (IDA) in women of reproductive age (WRA) and children under 5 years of age was obtained to inform priorities in health planning and policy in South Africa. We searched electronic databases for articles published between 1997 and 2021. A total of 713 articles were identified, of which 14 articles comprising 9649 WRA and 4085 children were included. Since most of the included studies were of low quality, we did not pool data in a meta-analysis due to heterogeneity (I2 textgreater 75%). In WRA, anaemia prevalence ranged from 22.0% to 44.0%; ID from 7.7% and 19.0%; and IDA from 10.5% to 9.7%. The prevalence of anaemia in pregnancy was 29.0% to 42.7%; and 60.6% to 71.3% in HIV-infected pregnant women. Three national surveys reported anaemia in children at 28.9%, 10.7%, and 61.3%, respectively. Overall, among the children under 5 years old, anaemia was more prevalent in 1-year-olds (52.0%) compared to the other age groups. Between 2005 and 2012, ID increased by 3.8% and IDA decreased by 83.2% in children. Anaemia in WRA and children under 5 years in South Africa was a moderate public health concern. Therefore, interventions addressing anaemia should be intensified, and policies on iron supplementation and food fortification need to be revised and aligned to the WHO multiple micronutrient supplementation recommendations.