The facility will be developed at Springs Branch railway sidings in Ince-in-Makerfield. An existing freight yard will be adapted to stable and maintain 24 electric and eight diesel trains.
The development, which is part of the Great North Rail Project, will be brought into use from December 2019.
Lauren Jones, scheme project manager at Network Rail, said: "At Springs Branch sidings, we're investing £46m to enhance an existing site by the West Coast main line by building brand new train maintenance facilities for Northern.
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"This brand new depot that forms part of the Great North Rail Project not only delivers a jobs boost for Greater Manchester, but the facilities it will provide will help transform passenger journeys across the north."
Ben Ackroyd, Engineering Director at Northern, said: "The new maintenance depot is a key part of our wider modernisation programme.
"By 2020 we will have retired all Pacers, refurbished our entire fleet and, of course, will have introduced our brand new electric and diesel trains. We will need state-of-the-art facilities to look after these trains and Springs Branch is a key part of this."
(LM/MH)
