The opposition for the August 5 match is not yet known but is likely to be a leading African national team, the London club said on their website (www.arsenalfc.com) on Friday.
The friendly will be played at the 60,000-capacity Abuja National Stadium.
Arsenal, who are also planning pre-season games in China, Malaysia and Hong Kong, last visited Africa for a tour of South Africa in 1993.
The Islamist group Boko Haram has been fighting a low-level insurgency in Nigeria for more than two years.
Although its attacks are mostly in the north of Africa's most populous nation it has bombed several targets in the capital Abuja, located in the centre of the country.
The office of local newspaper This Day was hit on April 26 by a car bomb and last year United Nations headquarters and the office of the chief of police were struck by suicide bombers.
The sect, which wants to impose an Islamic state on Nigeria's evenly mixed population of Muslims and Christians, has been blamed for hundreds of killings since its uprising against the government in 2009.