The patient had recently entered the country by plane from Uganda and had been treated for several days at a private hospital in the area of the capital Abuja, the health ministry said on Tuesday.
The woman is now in isolation and was infected with the Bundibugyo strain of the Ebola virus, the predominant variant in the current Ebola outbreak in Africa. It is particularly difficult to contain, as there is neither a vaccine nor a targeted treatment available.
The outbreak is spreading across the region. Kenya recently confirmed its first case and has since recorded nine infections and one death.
Dr Jean Kaseya, director general of the Africa Centers for Disease Control, said on X "we are facing an extremely serious threat", with a fatality rate of nearly 50 per cent of cases.
"This Bundibugyo Ebola outbreak has already become the most geographically extensive in history, affecting several countries spread across three regions of Africa," he said.
Nigeria's government has called on all public and private health facilities in the country of some 220 million people to maintain "highest vigilance".
Nigeria is the fourth African country in which cases of the Bundibugyo variant have been reported during the current Ebola outbreak, which began in mid-May in the Democratic Republic of Congo. There, 9,552 cases and 4,602 deaths are currently recorded, according to the health authority.
Uganda, which borders Congo and Kenya, also had 20 confirmed Ebola cases in total, which were traced back to one patient from Congo. Two patients died.
with AP