The patient is an Italian citizen who works in Nigeria and flew into the commercial city of Lagos from Milan on 25 February.
Authorities say he is stable with no serious symptoms and is being treated at a hospital in the city.
Elsewhere on the continent, Algeria and Egypt have also confirmed cases of the disease.
The World Health Organization (WHO) had warned that Africa’s “fragile health systems” meant the threat posed by the virus was “considerable”.
Meanwhile, South Africa’s health ministry has announced that two nationals aboard a cruise ship docked in Japan have tested positive for the virus.
In Kenya, the High Court has ordered the temporary suspension of flights from China following a petition by the Law Society of Kenya.
It comes amidst public outrage after China’s Southern Airlines resumed flights to Nairobi amid concern about the spread of coronavirus.
Globally, more than 80,000 people in nearly 50 countries have been infected. Nearly 2,800 have died, the vast majority in China’s Hubei province.