The Sky Sports pundit hit out on Wednesday morning, claiming he bought a ticket online but was turned away at Euston because he did not have the receipt.
Mr Neville said, when he tried to buy a replacement, he was told he had to return to the main desk to get one, despite the staff member apparently having a machine.
The frustrated former Manchester United star blasted the firm on his Twitter account to 3.61 million followers.
He fumed: "You are a joke @VirginTrains."
When asked by the firm what the problem was, he replied: "You've got a train manager called Simon who apparently can't sell tickets at the gate?
@VirginTrains You've got a train manager called Simon who apparently can't sell tickets at the gate? Now I've missed the train!!— Gary Neville (@GNev2) April 19, 2017
"Now I've missed the train!!"
Advised by a follower to buy a ticket online, he replied: "I did.
"I collected my tickets at the station and he said receipt missing!
"He said go buy another!"
Sharing a photo of the troublesome tickets, he ranted: "That's what the machine gave me (apparently one missing) he wouldn't sell me another.
"That's what the machine gave me. Simon said can't let you on.
"I said I will buy another now then! No go to the office. He had a machine!!"
A spokesman for the firm told the Daily Mail: "We always love to see football legends on our trains.
"But regardless of how many trophies they've won, all our customers need a valid ticket for travel and should leave plenty of time to board their train."