High vaccine wastage can serve as a critical barrier to achieving the gains of vaccination, especially in a country like Nigeria, where data on vaccine wastage are sparsely available. We determined the country-wide vaccine wastage rates and their determinants through a mixed-methods study conducted across 576 health facilities (primary and secondary) in 24 states in Nigeria. We collected facility-based immunization records from June 2018 to May 2019, in addition to healthcare workers' interviews and observations of fixed and outreach sessions. The results show that open-vial wastage ranged from 21.2% (95% CI: 20.2%, 22.2%) for the pentavalent vaccine to 72.6% (95% CI: 71.5%, 73.6%) for BCG. Open-vial wastage rates for BCG, measles, and yellow fever vaccines were higher during outreach sessions, with rates of 76.2%, 64.3%, and 65.2%, respectively. For the outreach and fixed sessions, PCV and Penta had the least wastages of 22.0% for fixed sessions and 20.4% for outreach sessions. This study identified vaccine presentation (liquid vs. lyophilized vaccines), vial size (4 dose vs. 5 dose vs. 10 dose vs. 20 dose), RI service delivery strategies (fixed vs. outreach sessions), number of children vaccinated, and human resources (healthcare workers position/cadre) as key determinants of vaccine wastages in Nigeria.