While safe and efficacious COVID-19 vaccines have achieved high coverage in high-income settings, roll-out remains slow in sub-Saharan Africa. By April 2022, Nigeria, a country of over 200 million people, had only distributed 34 million doses. To ensure the optimal use of health resources, cost-effectiveness analyses can inform key policy questions in the health technology assessment process. We carried out several cost-effectiveness analyses exploring different COVID-19 vaccination scenarios in Nigeria. In consultation with Nigerian stakeholders, we addressed three key questions: what vaccines to buy, how to deliver them and what age groups to target. We combined an epidemiological model of virus transmission parameterised with Nigeria specific data with a costing model that incorporated local resource use assumptions and prices, both for vaccine delivery as well as costs associated with care and treatment of COVID-19. Scenarios of vaccination were compared with no vaccination. Incremental cost-effectiveness ratios were estimated in terms of costs per disability-adjusted life years averted and compared to commonly used cost-effectiveness ratios. Viral vector vaccines are cost-effective (or cost saving), particularly when targeting older adults. Despite higher efficacy, vaccines employing mRNA technologies are less cost-effective due to high current dose prices. The method of delivery of vaccines makes little difference to the cost-effectiveness of the vaccine. COVID-19 vaccines can be highly effective and cost-effective (as well as cost-saving), although an important determinant of the latter is the price per dose and the age groups prioritised for vaccination. From a health system perspective, viral vector vaccines may represent most cost-effective choices for Nigeria, although this may change with price negotiation.