The attack happened at the Forward Operation Base in Ngwom village, some 14 kilometres (nearly nine miles) north of the Borno state capital, Maiduguri.
"Boko Haram infiltrated our base in Ngwom yesterday (Friday) at around 6:50 pm (1750 GMT) in which we lost three soldiers," a military officer in Maiduguri told AFP.
A second military source said the Islamist militants left with two army vehicles and "demobilised" a mine-resistant armoured vehicle.
"The terrorists also burnt two houses and a car belonging to our members in the village," added a civilian militia leader in Maiduguri.
It was not immediately clear which of the two Boko Haram factions was behind the attack.
Most of the attacks on troops in Borno and neighbouring Yobe state since mid-2018 have been claimed by, or blamed on, the self-styled Islamic State West Africa Province.
Others, though, have been carried out by fighters loyal to long-time factional leader Abubakar Shekau.
Nigeria's military has strongly denied claims the assaults on soldiers are an indication the group is resurgent, after repeated claims they were "technically defeated".
The attacks underline the persistent threat from the group, including to civilians, nearly 10 years after the start of the insurgency.
More than 27,000 people have been killed in northeast Nigeria and some 1.8 million others remain homeless.
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