Police in Bauchi state confirmed overnight witness reports of a huge explosion at the terminal in the town of Azare at 9:45 pm .
Area resident Musa Babale said the blast "shook buildings" and sent locals rushing for shelter.
"The whole place was a mess," he told AFP after visiting the site late Wednesday.
Bauchi police spokesman Mohammed Haruna said the bomb killed five people, leaving them "burnt beyond recognition," and that 12 others were injured.
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While there was no immediate claim of responsibility, Bauchi has been one of the hardest hit areas in Boko Haram's five-year uprising against the Nigerian state.
Bus station bombings have also become something of a hallmark for the insurgent group after twin attacks at a terminal on the outskirts of the capital Abuja earlier this year killed nearly 100 people.
The station in Azare, a town roughly 200 kilometres from the state capital Bauchi city, is a widely used transit point by travellers coming from Nigeria's embattled northeast, which has been under a state of emergency since May of last year.
Azare saw a series of attacks blamed on Boko Haram through 2012, while Bauchi has been consistently targeted throughout the uprising, including through church bombings, coordinated gun raids and notably a massive prison raid in 2011.
Any indication that the latest explosion was tied to Boko Haram will further undermine the government's claim to have negotiated a ceasefire with the extremist group.