Background: The World Health Organisation (WHO) Africa region experiences multiple public health emergencies (PHEs) annually. PHEs have been documented to affect the provision of health services including immunisation. To our knowledge, there is a scarcity of studies characterising PHEs and the performance of national immunisation programmes (NIPs) in countries within the WHO Africa region that have experienced PHEs. This study assessed PHEs (armed conflicts, disasters, and disease outbreaks) and the performance of NIPs in the context of PHEs using global and regional immunisation targets. Methods Countries in the WHO Africa region that were reported to benefit from the African Public Health Emergency Fund (APHEF) were used as case studies. Data on PHEs and immunisation indicators recorded between 2010 and 2019 in the study countries were extracted from different electronic PHE databases (the Emergency Events database, the Uppsala Conflict Data Program, the WHO Emergency Preparedness and Response, and the Program for Monitoring Emerging Diseases Mail) 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 in the selected countries from 2010 to 2019. Statistical significance was defined at p-value < 0.05. Results Thirteen countries were included in this study. A total of 175 disease outbreaks, 288 armed conflicts, and 318 disasters were reported to have occurred within the 13 countries from 2010 to 2019. 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 statistically significantly (p=0.03) associated with not attaining MNT elimination. Conclusion PHEs are prevalent in the WHO Africa region, irrespective of the level of a country's immunisation maturity. In absence of effective interventions, PHEs have the potential to derail the progress of NIPs in the WHO Africa region. As we enter the Immunisation Agenda 2030 era, this study advocates for the prioritisation of interventions to mitigate the impacts of PHEs on the NIPs.