Background In the World Health Organisation African region (WHO-Afro), multiple public health emergencies (PHEs) are experienced annually. PHEs are known to affect the provision of health services including immunisation. To our knowledge, there is limited information on the characterisation of PHEs and the performance of national immunisation programmes (NIPs) in countries within the WHO-Afro. This study assessed PHEs (armed conflicts, disasters, and disease outbreaks) and the performance of NIPs within PHE contexts using global and regional immunisation targets.MethodsCountries recorded to have benefitted from PHE mitigation funds from the African Public Health Emergency Fund (APHEF) were used as case studies. Data on PHEs and immunisation indicators between 2010 and 2019 in the selected countries were extracted from different PHE electronic databases and the WHO/UNICEF immunisation database, respectively.The PHEs and immunisation indicators were stratified by country and summarised using descriptive statistics. The Mann-Whitney U test was carried out to determine the association between the frequency of PHEs and the performance of NIPs. Statistical significance was defined at p-value < 0.05. ResultsBetween 2010 and 2019 there were a total of 175 disease outbreaks, 288 armed conflicts, and 318 disasters in the 13 countries selected as case studies. The Democratic Republic of Congo had the highest total PHE count (n=208), while Liberia had the lowest (n=20). Only three of the 13 countries had a median coverage value for the third dose of the combined Diphtheria, Tetanus, and Pertussis vaccine (DTP3) that had attained the target for ≥90% immunisation coverage.Higher counts of armed conflict and total PHEs were associated with not meeting the immunisation targets for national DTP3 coverage of ≥90% and Maternal and Neonatal Tetanus (MNT) elimination, p<0.01. Higher disaster counts were also associated with not attaining MNT elimination, p=0.03.ConclusionPHEs are prevalent in the WHO-Afro, irrespective of the level of a country’s immunisation maturity. In absence of effective interventions, the PHEs have the potential to derail the progress of NIPs in the WHO-Afro. As we transition towards the Immunisation Agenda 2030, we recommend that the WHO-Afro prioritises interventions to mitigate the impacts of PHEs on the NIPs.