Operated by Arriva Rail, the services have been hit by poorly implemented timetables, delays, strikes and the late delivery of new trains.
The government’s ‘Operator of Last Resort’ (OLR) already runs the East Coast network under the LNER brand following the demise of Virgin Trains East Coast.
In January, Transport Secretary Grant Shapps said the Northern franchise was “no longer financially sustainable”.
In this week’s announcement, Shapps said: “This is a new beginning for Northern, but it is only a beginning.
“Northern’s network is huge and complex and some of the things which are wrong are not going to be quick or easy to put right. But I am determined that Northern passengers see real and tangible improvements across the network as soon as possible.”
Shapps added: “Today marks the first small step towards the north taking back control of its railways and its people taking back control of their travelling lives.”
The news comes in the same week that the BBC reported the government’s unpublished official review into HS2 “strongly advises against cancelling” the project.
The proposed high-speed rail network from London to Birmingham and on to Manchester and Leeds has been criticised for its spiralling cost, which could be twice the original 2015 estimate of £56billion.