Police say the teenage bomber detonated early Tuesday in Adamawa state as people were arriving for prayers.
"Some of the dead were in pieces beyond recognition", said Bayi Muhammad, a worshipper at the mosque in Mubi who said he only escaped the blast because he was late for early morning prayers.
Abubakar Othman, a police spokesman in Adamawa state, said the death toll is at least 50 but "there could be more as those seriously injured could add to the figure".
Some 20,000 people have been killed in Boko Haram's eight-year insurgency.
In October 2012, at least 40 people were killed in an attack on student housing in Mubi that was widely blamed on Boko Haram. "The group has used children as young as five to carry out hundreds of attacks on busy marketplaces, checkpoints and mosques in the past few years", the British newspaper said.
Nigeria mosque suicide bombing leaves 50 dead
While Nigeria's military in recent months has flushed Boko Haram from its forest stronghold, President Muhammadu Buhari's claim late previous year that the extremist group had been "crushed" has proven to be premature. A suicide bomber detonated an explosive device just after the mosque, said a prayer.
Attacks on isolated rural communities have been a feature of Boko Haram's Islamist insurgency in the remote region in recent months after the end of the annual rainy season.
But it has been peaceful since the military and the civilian militia ousted them from the town, which is a commercial hub and home to the Adamawa State University.
Boko Haram typically mounts suicide attacks in crowded public places such as mosques and markets.
Boko Haram fighters are also said to be hiding in the Mandara mountains, which forms the border of Adamawa and Nigeria with neighbouring Cameroon, where there has also been more attacks.
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