The head of the Borno state emergency management agency, Ahmed Satomi, said the blast happened at about 5:30 am (0430 GMT) in the London Ciki area of Maiduguri, which has been at the epicentre of Boko Haram violence since 2009.
When she approached the mosque, they demanded that she stop to be searched but she suddenly bolted into the mosque and set off her bombs.
Three other female suicide bombers were located in Maiduguri at about the same time, said Satomi.
Two were killed in the Mammanti area as they tried to cross the ditch around the city perimeter while another set off her explosives in the suburb of Simari, he added.
It is the second time in a week that four female suicide bombers have disrupted the city of Maiduguri.
Last Monday, at least 19 people were killed and 23 others injured when four women set off their bombs in the Molai Kolemari area of the city.