It was revealed last week how a guard aboard a service along the East Coast Main Line apparently took a swipe at the town by announcing: "As if it wasn't miserable enough already, the next station stop is Doncaster."
Now the rail giant has apologised for the remarks, describing them as "playful."
A Virgin spokesman said: “Our staff are encouraged to be friendly and playful with the announcements.
"We apologise if this particular announcement caused offence. It certainly wasn’t our intention – We love Doncaster!”
The row erupted when passenger Mark Davies, who was aboard a Virgin Trains express from London King's Cross to York last Monday, heard the remarks as the train approached Doncaster.
He said: "Just as we were coming in, this guy came on the intercom and said "if today wasn't already miserable enough, the next station stop is Doncaster."
The 13.08 service from the capital along the East Coast Main Line had already battled through torrential rain and strong winds and Mark, 45, from York, said the conductor's remarks were referencing the weather - but he didn't see the funny side.
He said: "I understand that he was probably trying to be funny, but I don't think it was his place to be disparaging and make an unnecessary put down.
"It might just have been a joke and light-hearted comment but I found it a bit sarcastic. I've travelled on trains plenty but never heard an announcer make their thoughts clear on what they think of a place.
"It all seemed a bit unprofessional."
Mark, a traffic surveyor, called his friend Robert Wainman to tell him of the announcement and the proud Doncastrian instantly sprung into action, contacting Doncaster MPs Ed Miliband, Rosie Winterton and Caroline Flint and the managing director of Virgin Trains to make a complaint.
Doncaster-born Robert, who lives in Selby, said: "I've got a strong attachment to Doncaster and don't like people having a dig and criticising it.
"Doncaster has got a very proud railway history so its not on when someone is making cheap digs. I know the guy probably thinks he was just being funny, but it's not on."
Mark says that further remarks came as the train pulled into York with the guard announcing: "We are now arriving into York, which is in a different time zone so please put your watches back 25 years."
He added: "I don't want to get the guy sacked, but I just don't think its right and doesn't portray Virgin in a great light."