Objective: To estimate the prevalence of missed opportunities for vaccination (MOV) among children aged 0–23 months attending health-care facilities in Africa and explore the factors responsible for MOV using systems thinking.

Research design and methods: We conducted a systematic review and meta-analysis of studies reporting the proportion MOVs. Five electronic databases were searched. A random effects model was fitted to obtain pooled estimates of MOV and a causal loop diagram (CLD) was constructed to explore the dynamics of the causes of MOV. MOV was defined as any contact with health services in Africa, by an unvaccinated or under-vaccinated child, aged 0–23 months, who is eligible for vaccination and free of any contraindication, which does not result in vaccination.

Results: Four hundred and twenty-one publications were found, of which 20 studies from 14 countries were included. The pooled prevalence of MOV was estimated to be 27.26% (95%CI: 18.80–36.62). A CLD with seven reinforcing and two balancing loops were constructed.

Conclusion: Our findings suggest that about one in every four children under the age of two years who visited health facilities in 14 African countries missed the vaccination they were eligible to receive. To enable continent-wide estimates, more MOV assessments are required.