Background: Deaths due to vaccine-preventable diseases are one of the leading causes of death among African children. Vaccine coverage is an essential measure to decrease infant mortality. The COVID-19 pandemic has affected the healthcare system and may have disrupted vaccine coverage. Methods: DTP third doses (DTP3) Vaccine Coverage was extracted from UNICEF databases from 2012 to 2021 (the last available date). Joinpoint regression was performed to detect the point where the trend changed. The annual percentage change (APC) with 95% confidence intervals (95% CI) was calculated for Africa and the regions. We compared DTP3 vaccination coverage in 2019–2021 in each country using the Chi-square test. Result: During the whole period, the vaccine coverage in Africa increased with an Annual Percent change of 1.2% (IC 95% 0.9–1.5): We detected one joinpoint in 2019. In 2019–2021, there was a decrease in DTP3 coverage with an APC of −3.5 (95% −6.0; −0,9). (p< 0.001). Vaccination rates decreased in many regions of Sub-Saharan Africa, especially in Eastern and Southern Africa. There were 26 countries (Angola, Cabo Verde, Comoros, Congo, Côte d’Ivoire, Democratic Republic of the Congo, Djibouti, Ethiopia, Eswatini, The Gambia, Guinea-Bissau, Liberia, Madagascar, Malawi, Mauritania, Mauritius, Mozambique, Rwanda, Senegal, Seychelles, Sierra Leone, Sudan, Tanzania, Togo, Tunisia, Uganda, and Zimbabwe) where the vaccine coverage during the two years decreased. There were 10 countries (Angola, Cabo Verde, Comoros, Democratic Republic of the Congo, Eswatini, The Gambia, Mozambique, Rwanda, Senegal, and Sudan) where the joinpoint regression detected a change in the trend. Conclusions. COVID-19 has disrupted vaccine coverage, decreasing it all over Africa.