There will be no Southern Rail services between Clapham Junction and Milton Keynes Central, which goes through Wembley Central on 19 May, after Network Rail designated the weekend for planned engineering works.
These have since been cancelled, but not in enough time for Southern to staff the services which would normally run.
A tweet from one of the Southern Rail team said: “I have been informed that due to the lateness of the decision to cancel the works it is not possible for us to adjust the crew plans and run services on this route at the weekend.
“It does appear the info on the website is incorrect and we will update.”
A Southern Rail spokesman told Sky News: “We are looking hard at whether we can run a service but the late notice of these changes does mean it will be very difficult to adjust plans for train crew who would have already been allocated work elsewhere.”
The FA Cup final, between Chelsea and Manchester United, kicks off at Wembley at 5.15pm, with tens of thousands of fans heading to northwest London.
The planned engineering works were also meant to affect London Overground services between Clapham Junction and Willesden Junction. The TfL website still says there will be no service between the two stations.
In addition, the District line, which intersects the Overground at West Brompton, will not be running between South Kensington, Edgware Road and Wimbledon, Kensington Olympia, Ealing Broadway, Richmond.
The Circle, Bakerloo, and Docklands Light Railway all have planned closures in place as well.
Caroline Pidgeon, the Liberal Democrat assembly member and chairman of the Transport Committee, said: “The weekend of 19 and 20 May will be a very special weekend for the capital, with a London team in the FA Cup final and many people coming to London to take part in events across the capital celebrating the royal wedding.
“On such an important weekend of sport and celebration it is a great shame that poor planning and coordination by Transport for London and Network Rail runs the risk of creating so much disruption and inconvenience for Tube and rail travellers.”
A Network Rail spokesman told the Evening Standard: “We have been working closely with train operators and the police in the lead-up to the royal wedding.
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“We have no planned engineering works taking place on routes to Windsor and will have extra staff on hand at Paddington, Waterloo and Reading stations.”
:: Sky News is broadcasting live from Windsor with all the build-up to the royal wedding, with exclusive live coverage of the wedding in UHD in a special programme from 9am to 3pm on Sky News and Sky One this Saturday.