
The BBC's Bilkisu Babangida in Maiduguri says the move follows strong rumours that the group plans to attack the campus.
Boko Haram opposes Western education and fights for Islamic rule.
In recent weeks, about 40 people have been killed in attacks blamed on the group.
On Tuesday morning, a military patrol was targeted in Maiduguri.
In the ensuing confusion, four people were shot dead and two soldiers wounded.
There has also been a blast at a church in the town of Suleja, near the capital, Abuja.
No casualties have been reported.
Last month, Boko Haram bombed the police headquarters in Abuja, killing at least six people.
Our reporter says Maiduguri, a Boko Haram stronghold, is gripped by fear with many people staying indoors.
Residents are worried that the military will carry out indiscriminate arrests as they search for the attackers, she says.
'Motorbike ban'University authorities said they had closed the campus because of the growing insecurity in Maiduguri.
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Many residents are, however, fleeing Maiduguri.
Bus stops are overcrowded and some people are leaving on foot with their belongings and livestock, correspondents say.
On Saturday, residents told the BBC that soldiers had dragged men out of their homes before setting their properties on fire.
The military accuses some residents of giving sanctuary to Boko Haram fighters.
Residents have also been ordered to walk with their hands raised as they approach military checkpoints in the city, correspondents say.
Last week, Maiduguri banned all motorbikes to prevent drive-by shootings by Boko Haram.
Boko Haram gunmen often use motorbikes to assassinate security officers and politicians.
The group's official name is Jama'atu Ahlis Sunna Lidda'awati wal-Jihad, which in Arabic means "People Committed to the Propagation of the Prophet's Teachings and Jihad".
But residents of Maiduguri, where it was formed in 2002, dubbed it Boko Haram.
Loosely translated from the local Hausa language, this means Western education is forbidden.
Residents gave it the name because of its strong opposition to Western education, which it sees as corrupting Muslims.
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