In Nigeria, Africa’s most populous country, the concept of japa in which people flee harsh economic circumstances in quest of better possibilities, has become more common. This study investigates the critical problem of brain drain in Nigeria as the largest populated country in Africa, concentrating on the reasons that contribute to the phenomena, such as a lack of access to lucrative opportunities and widespread inequality. The study examined the dynamics of migration using a mathematical model that accounts for the population of the emigration source, the number of opportunities at the source, the size of the emigration population, and the population of returnees. We estimated the model’s parameters based on actual data from trusted sources. We derived and explained the basic emigration number, emigration-free, and persistent emigration equilibrium states of the model. Sensitivity studies were used to understand how different model parameters affect the emigration rate and the basic emigration number. This analysis highlights the relationship between economic, societal, and personal factors that influence migration, providing valuable insights for policymakers and scholars addressing migration issues. Our findings emphasize the necessity of developing equitable opportunities to mitigate brain drain and suggest strategies for retaining talent within the country.