One of the routine health services that is being disrupted by coronavirus disease 2019 (COVID-19) in Africa is childhood immunization. This is because the immunization system relies on functioning health facilities and stable communities to be effective. Its disruption increases the risk of epidemics of vaccine-preventable diseases, which could increase child mortality. Therefore, policymakers must quickly identify robust and context-specific strategies to rapidly scale-up routine immunization in order to mitigate the impact of COVID-19 on their national immunization performance. To achieve this, we propose a paradigm shift towards systems thinking and use of implementation science in immunization decision-making. Systems thinking can inform a more nuanced and holistic understanding of the interrelationship between COVID-19, its control strategies, and childhood immunization. Tools like causal loop diagrams can be used to explicitly illustrate the systems structure by identifying feedback loops. Once mapped and leverage points for interventions have been identified, implementation science can be used to guide the rapid uptake and utilization of multifaceted evidence-based innovations in complex practice settings. As Africa re-strategizes for the post-2020 era, these emerging fields could contribute significantly in accelerating progress towards universal access to vaccines for all children on the continent despite COVID-19.