At least 14 people, including the girls, died and 39 were injured in the attacks at a mosque and house of vigilante leader, the military said.
More than 100 people died in similar attacks in the city two weeks ago, the BBC reports.
Maiduguri is where Boko Haram Islamist militants were first based when they began their insurgency six years ago.
Some 17,000 people are said to have been killed in that time and attacks by the group have intensified since Muhammadu Buhari became president in May, vowing to defeat the insurgents.
The BBC says people were waiting for the final evening prayers when the suicide bombers struck the mosque.
Officials, according to reports, fear that the number of those who lost their lives is likely to rise.
Witnesses and security sources said some of the girls were as young as nine. -The Nation