This study examined the association between COVID-19 and fear of contracting COVID-19 and reasons for vaccination refusal. A population-based online survey was conducted via social media in Nigeria using the Fear of COVID-19 scale and items related to vaccination refusal/hesitancy items. Individuals aged 13 years and older were invited to participate. Data were analysed using binary logistic regression to calculate odds ratios (ORs) and associated 95% confidence intervals (CIs) at a p-value of less than 0.05. The study enrolled 577 individuals with a mean age of 31.86 years, 70% of whom were male and 27.7% of whom had received at least one dose of the vaccine against COVID-19. None of the variables on the Fear of COVID-19 scale significantly predicted vaccine uptake in multivariate analysis. However, individuals who were fearful of COVID-19 were more likely to be vaccinated in bivariate analysis (OR: 1.7, 95% CI: 1.06–2.63). The most significant factors among the vaccination refusal items associated with COVID-19 vaccination were doubts about vaccination (adjusted OR: 2.56, 95% CI: 1.57–4.17) and misconceptions about vaccine safety/efficacy (adjusted OR: 2.15, 95% CI: 1.24–3.71). These results suggest that uptake of the vaccine against COVID-19 in Nigeria can be predicted by factors associated with vaccination refusal, but not by fear of COVID-19. To contain the pandemic COVID-19 in Nigeria, efforts should be made to educate people about the efficacy of the vaccine and to increase their confidence in vaccination.