Background: Nigeria, the most populous country in Africa, has reported relatively high levels of alcohol misuse, yet limited resources to guide effective population-wide response. There is a need to integrate existing empirical information in order to increase the power and precision of estimating epidemiological evidence necessary for informing policies and developing prevention programs. Objectives: We aimed to estimate nationwide and zonal prevalence of harmful use of alcohol in Nigeria to inform public health policy and planning. Methods: Epidemiologic reports on alcohol use in Nigeria from 1990 through 2018 were systematically searched and abstracted. We employed random-effects meta-analysis and meta-regression model to determine the number of harmful alcohol users. Results: 35 studies (n = 37,576 Nigerians) were identified. Pooled crude prevalence of harmful use of alcohol was 34.3% (95% CI: 28.6-40.1); twice as high among men (43.9%, 31.1-56.8) compared to women (23.9%, 16.4-31.4). Harmful alcohol use was higher in rural settings (40.1%, 24.2-56.1) compared to urban settings (31.2%, 22.9-39.6). The number of harmful alcohol users aged ≥15 years increased from 24 to 34 million from 1995 to 2015. However, actual age-adjusted prevalence of harmful use of alcohol in Nigeria decreased from 38.5% to 32.6% over the twenty-year period. Conclusions: While the prevalence of the total population that drinks harmfully appears to be dropping, absolute number of individuals that would be classified as harmful drinkers is increasing. This finding highlights the complexity of identifying and advocating for substance abuse policies in rapidly changing demographic settings common in Africa, Asia, and other developing countries.