The attack happened in the early evening in Dapchi village in the Bursari area of Yobe state, which is in the conflict-torn northeast of Nigeria.
The latest attack comes days after Chief of Army Staff; Tukur Buratai, placed a N3 million bounty on Abubakar Shekau, factional leader of the Boko Haram sect.
"We have received a directive from the state government to close the school and allow the parents to take their children back home until peace returned to the school".
"They shot sporadically and forced the school food store opened".
The militants reportedly looted the buildings after finding the school empty.
The attack recalls Boko Haram's audacious kidnapping of more than 200 schoolgirls from the town of Chibok in April 2014.
A teacher who escaped said the gunmen stormed the school around 7pm through the eastern part of the town.
Abdulmaliki Sumonu, the Yobe Commissioner of Police, said on Tuesday that there was no loss of live in the attack on Government Girls College in Dapchi town. "We and the students ran into the bush for safety".
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A member of a local civilian militia that tackles Boko Haram said: "Military jets were deployed and are in pursuit".
No schoolgirl abducted at Dapchi by Boko Haram attackers.
Fifty-seven escaped in the immediate aftermath.
Haruna Yahaya, 35, was sentenced to 15 years in prison on Friday for masterminding the abductions, which caused global outrage.
A total of 205 Boko Haram militants have been convicted and 526 others freed for lack of evidence in the second round of mass trials of persons arrested in connection with the insurgency in northeast Nigeria, according to a statement.
Jail terms ranged from three to 60 years, said the ministry.
The group has consistently attacked education.