Harmattan is a season of dry, cold, dusty wind, and haze that is peculiar to West Africa. This season and COVID-19 share common conditions such as malaise and respiratory issues like as runny nose, cough and sneezing, and raise a question of a possible relationship that begs to be answered. This study investigated whether the meteorological factors of humidity and wind speed during harmattan have association with COVID-19 incidence and mortality in the 2 major COVID-19 epicenters of Lagos state and the Federal Capital Territory (FCT) in southern and northern geopolitical regions of Nigeria respectively. Data used were from March, 2020 to February, 2022, which corresponded to the period of 2 years after the first case of COVID-19 was detected in Nigeria. Correlation analysis was performed using incidence or mortality data on COVID-19 over the duration of 2 years and during the harmattan periods, as well as the humidity and wind speed data for the corresponding periods. Our results showed that there was no significant correlation between the humidity or wind speed and COVID-19 daily incidence or mortality during the harmattan and non-harmattan periods in Lagos state. In the FCT however, there was a significant positive correlation between humidity and COVID-19 incidence, as well as a negative correlation between wind speed and COVID-19 incidence. No significant correlation existed between humidity or wind speed and daily mortality. Taken together, the findings of this study show that weather components of the harmattan season have association with COVID-19 incidence but not mortality, and the association could vary depending on location.