From January 2020 to December 2020, the South African national non-polio acute flaccid paralysis rate was 2.6/100 000 children under 15 years compared to 3.5/100 000 children in 2019. The country reached the World Health Organization target of 2.0/100 000 population under the age of 15, but did not reach the country’s target of 4.0/100 000. Receipt of samples in the laboratory within 72 hours of collection was 36%, below the World Health Organization’s target of 80%. No wild-type poliovirus nor vaccine-derived poliovirus was detected in South Africa. Sabin poliovirus type 2 and circulating vaccine-derived poliovirus type 2 (cVDPV2) were detected from 13 African countries, namely Burkina Faso, Angola, Malawi, Ethiopia, Senegal, Côte d’Ivoire Niger, the Democratic Republic of the Congo, Republic of South Sudan, Zambia, Guinea, Sierra Leone and Mali. Sabin 2 and cVDPV2 were the most prevalent poliovirus strains in the African region. The performance of AFP surveillance in 2020 has declined despite the fact that South Africa has achieved the WHO target. There is an urgent need for more African countries to use novel oral poliovirus 2 vaccines to prevent cVDPV2 outbreaks. The percentage of South African samples arriving at the laboratory within 72 hours was below the WHO target. There is also an urgent need to improve the logistics of sample transportation to the laboratory within the required time. As the Global Polio Eradication Initiative winds down and devolves to regional WHO initiatives, incorporation of national AFP surveillance targets into integrated disease surveillance will require attention.