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The firm is reinstating 75% of the routes it withdrew after its new timetable caused disruption.
Services cancelled following a timetable shake-up at Northern rail have begun running again.
Northern scrapped 168 services per day last month to try to relieve chaos caused by the timetable's introduction in May.
Services in Manchester, Merseyside and Lancashire are partially resuming while all trains on the Lakes Line, in the Lake District, are being reinstated.
The remaining 25% of its cancelled trains do not restart until September.
The company, which has faced calls for it to be stripped of its franchise, says a "more gradual" reintroduction will ensure a more stable and reliable service.
What went wrong with the timetable changes?
However, Greater Manchester Mayor Andy Burnham has written to the prime minister, asking her to personally intervene over the "chaos" caused by Northern this summer.
He said: "People could have legitimately expected, when fewer trains were running, that at least the ones that were running would be on time, well they haven't been. The emergency timetable didn't solve anything.
"And then on Saturday night, nine o'clock an email lands saying Northern will cancel 47 services tomorrow so we can get trains in the right place for Monday morning.
"Even if trains do run better today it's because there were no services yesterday.
"Speak to any commuter in the north west of England and they will tell you that Northern services were poor for a long time before the new timetable came in and they haven't got much better in the two months since.
"If you turn up at a train station it's effectively a lottery."
A government spokesman said: "The Rail North Partnership has accepted the rail industry's recommendation to phase in services from Monday when 75% of the Northern train services removed during the interim timetable will be reintroduced.
"This is in addition to further adjustments to timetables to improve reliability, so that passengers can better plan ahead."
He added that Mr Burnham sits on the board of Transport for the North "which jointly manages the Northern franchise through the Rail North Partnership".
Thousands of passengers have applied for compensation from Northern, which made the first pay-outs last week.
On Monday morning, passengers said there were still delays and cancellations.
David Jenkins posted on Twitter: "First train for 2 months and they cancel it two mins after it's meant to arrive."