On other days, rail replacement services will arrive and depart from Crewe station, so passengers have been urged to check details of their journey.
NR said the work involves Basford Hall lines, which take freight trains around the station and back onto the West Coast Main Line, in order to “efficiently transport essential goods up and down the country, for years to come”.
Important drainage and track work, as well as a full re-signalling in the area has also been undertaken, it said.
Programme manager Jamie Morris said: “We have worked hard to reduce the impact on passengers as much as possible, which means there is a different timetable on different days during this time.
“I am grateful to passengers and the community of Crewe for their patience during this important work.”