The attack took place in Damaturu, the capital of Yobe state yesterday.
Eleven persons were killed when the sect members attacked Government Secondary School, Damaturu and a military checkpoint, military spokesman Lt. Eli Lazarus said.
Two teachers, seven students and two insurgents are those killed in the attack, he said, adding that three soldiers sustained severe injuries during the clash.
Eleven corpses were brought into his hospital, medical director of Damaturu Specialist Hospital Salem Umar said.
More From This Section
According to a survivor student, Goni Abubakar, the insurgents entered their school hostel in the evening and started shooting, forcing them to flee by jumping over the school fence.
Recently, Nigerian President Goodluck Jonathan declared a state of emergency in three states of Adamawa, Borno and Yobe where terror groups are known to be more effective.
Nigerian army moved in to the states and forcefully took over the camps where the groups organised themselves, especially in Borno, releasing women and children held as captives.
Boko Haram has been a major terrorist group in Nigeria which has killed thousands through suicide attacks, bombings and shootings.