Fourteen 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.
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's Abdullahi Kaura Abubakar in the capital, Abuja, says people were waiting for the last evening prayers when the suicide bombers struck the mosque.
Officials fear that the number of those who lost their lives is likely to rise, he says.
Witnesses and security sources said some of the girls were as young as nine.
Our correspondent says the attacks in Maiduguri, the capital of Borno state, come as the military says it is winning the war against Boko Haram.
The security forces have in recent months reclaimed territory captured by Boko Haram fighters and freed a number of people kidnapped by the militant group
