Services in Yorkshire, London, Manchester, Bristol, Edinburgh and Glasgow are among those affected.
Network Rail said it is carrying out the work over Easter as fewer passengers use the railways during that period.
More than 13,000 rail workers will be deployed on projects between Good Friday and Easter Monday.
As a consquence there will be a reduced TransPennine Express service running to and from York, Leeds, Huddersfield and Manchester from April 14 to 17.
Other engineering schemes taking place will include work on London’s new east-west rail service Crossrail, the Ordsall Chord to boost connections in Manchester and the modernisation of Bath Spa station in preparation for longer trains.
Network Rail’s managing director for England and Wales, Phil Hufton, said: “This Easter, thousands of rail workers will be working round the clock to deliver our Railway Upgrade Plan.
“This will provide faster, better services in the long run and help relieve overcrowding to respond to the huge growth on Britain’s railways.
“We know that many people want to use the railway during the Easter holidays and the good news is that over 95 per cent of the network is unaffected by this work.
“But there will be some services that are impacted and so we strongly advise passengers to plan their journeys in advance.”
It follows major disruption to a number of train services across Yorkshire on Monday this week due to industrial action.