The coronavirus disease of 2019 (COVID-19) is a pandemic that is ravaging Nigeria and the world at large. This data article provides a dataset of daily updates of COVID-19 as reported online by the Nigeria Centre for Disease Control (NCDC) from February 27, 2020 to September 29, 2020. The data were obtained through web scraping from different sources and it includes some economic variables such as the Nigeria budget for each state in 2020, population estimate, healthcare facilities, and the COVID-19 laboratories in Nigeria. The dataset has been processed using the standard of the FAIR data principle which encourages its findability, accessibility, interoperability, and reusability and will be relevant to researchers in different fields such as Data Science, Epidemiology, Earth Modelling, and Health Informatics.