The head of the Borno state emergency management agency, Ahmed Satomi, said the blast injured 15 others in the London Ciki area of Maiduguri, which has been at the epicentre of Boko Haram violence since 2009.
"The mosque was being guarded by civilian JTF [joint task force militia] during prayers," he told AFP.
"Unknown to them, the girl was being pursued from another part of town by residents who were suspicious of her movement at the time.
"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."
"There were two girls that wanted to attack the mosque but one of them got stuck in barbed wire in the ditch dug near the area. The second one escaped and began to run as our operatives there began to chase after her," said spokesman Danbatta Bello with the Civilian-JTF self-defence force.
"She rushed to the mosque and detonated the second bomb."
The mosque collapsed in the blast. Police did not immediately comment.
Two other female suicide bombers were shot and killed in Maiduguri around the same time as the mosque was attacked, Bello said.
It is the second time in a week that four female suicide bombers have sought to cause carnage in 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.
Boko Haram has increasingly used girls and young women to carry out attacks. Some young women who escaped the hardline group have said girls are drugged and forced to carry out suicide missions.
Nigeria's government late last year declared that Boko Haram had been "crushed" but deadly attacks continue. The Islamic group have killed more than 20,000 people, abducted thousands of others and spilled over into neighbouring countries.
Northeastern Nigeria is part of what the United Nations has called the world's largest humanitarian crisis in more than 70 years, with the World Food Programme estimating that more than 4.5 million people in the region need emergency food assistance. Boko Haram has disrupted both agriculture and markets.