The FA have decided on a 5.15pm kick-off for the Wembley showpiece meaning that fans travelling down from the North-West will either have to leave the match early or book an overnight stay in the capital if relying on the train.
The FA's decision to hold the match at that time has been described as "crackers" and was made with a "blatant disregard to the fans planning to attend" according to fans' groups of the sides involved.
Virgin said they warned the FA that the timing of the match would leave their customers in a difficult situation.
A Virgin spokesperson confirmed that: "Because of the possibility of extra time and penalties, Wigan and Manchester City supporters will be unlikely to see the end of the match and catch any advertised return service back to Wigan or Manchester that evening.
"The unpredictability of exactly when the match will end, coupled with the earlier close down of the route for essential maintenance and inspection means that the planning of any additional services is extremely difficult given the high numbers of supporters that would attempt to return to the North-West that evening."
Andrew Thomas, chairman of the Ashton-under-Lyne branch of the Manchester City Supporters Club told the BBC he thought the decision was "crackers."
"It is a game between two North-West teams - fans will have a four-to-six hour journey to get there and the same to get back," he said.
"With this late kick-off, anyone who was planning to travel by train will likely have to re-think because once the game is finished and you have had all the celebrations, people are not going to be leaving the stadium until gone eight.
"I would imagine they would struggle to get the last train back to the North-West."
Jason Taylor, Wigan Athletic Supporters Club spokesman added: "It just makes the day a lot longer and a lot more difficult for the fans that go.
"We are going to be using the same stretch of road to travel down, you could be talking up to 250 or so coaches all heading south, and they won't be getting back home until early in the morning."
It will be the second time the showpiece game will be played in the evening, following on from Chelsea's win over Liverpool last year and an FA spokesperson defended the move by saying "only a minimal amount of fans" use trains.
"The 5.15 pm kick-off time gives more people an opportunity to see the game and proved very popular last season," said the FA.
"A post-5pm kick-off slot on a Saturday has been used regularly by both the Premier League and Football League for their televised fixtures for a number of seasons.
"We have been in dialogue with Virgin about travel options back to the North-West since before the semi-finals although research shows that only a minimal amount of fans use this mode of transport when travelling to Wembley Stadium.
"National Express are the official coach partner of Wembley Stadium and their service was well received by fans at last season's FA Cup Final."
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