Officials said previously 10 people were killed and 47 were injured in Tuesday’s attack when jihadists fired rocket-propelled grenades on the densely-populated city.
Boko Haram has previously made incursions into Maiduguri, the capital of Borno state, using heavy guns and suicide bombers.
“The death toll has risen to 16,” Babakura Kolo, the leader of a self-defence militia, told AFP.
In one of the neighbourhoods affected, Gwange, nine boys were killed when one of the explosives landed in a field where they were playing football, Kolo said.
“Initially four died but five more died from the serious injuries they sustained from the explosion.”
Another militiaman, Umar Ari, gave the same death toll and said it could still rise as many were injured.
Eyewitness Sama’ila Ibrahim said the jihadists crossed the ditch fortification around Maiduguri, sending residents scrambling for safety with sporadic shooting.
Ibrahim said the militants came through Boboshe village, a known Boko Haram enclave.
Attacks by the group aimed at overrunning the regional capital are usually foiled in fierce gun battles with Nigerian troops.
In February last year, Boko Haram fired volleys of explosives into the city, injuring several people.
Since the insurgency began in 2009, the jihadist conflict has killed 36,000 people and displaced around two million from their homes in the region.