He becomes the sixth fatality in Nigeria, Africa's most populous country.
The doctor had treated a patient, who later recovered and had earlier met Patrick Sawyer, the man who took Ebola from Liberia to Nigeria. West Africa's health ministers are meeting later on Thursday to discuss how to tackle the world's most deadly Ebola outbreak.
The World Health Organisation (WHO) says the outbreak has already killed 1,427 people.
The WHO has said that it is the largest ever Ebola epidemic and has infected an estimated 2,615 people.
Liberia has been hardest hit of the affected countries, with 624 deaths and 1,082 cases since the start of this year. The virus is not airborne and is spread when humans come into contact with bodily fluids such as sweat and blood of those infected with the virus.
Till date, there is no vaccine or cure for the Ebola virus outbreak, the BBC report said.