Police cordoned off St Helen's Square in the centre of York on Saturday to protect the public and contain a group of up to 50 Tigers fans who had sparked trouble after arriving in the city by train.
The group had initially headed for a pub in Micklegate where York City fans had gathered, but were intercepted by police and herded into the Lendal Cellars pub, where they were held for about two hours.
Witness Sandra Preston said: "At first it sounded like a Viking procession going past and a lot of noise. I went to look and the next thing there was glass being smashed and police running at them with batons."
Two men from Hull and one from York were arrested for disorder offences.
Police later escorted the Hull fans to York railway station where they were put on a train and escorted back to Hull.
Supt Lisa Winward, from North Yorkshire Police, said: "This was a pre-season friendly match and we had no indications that there would be any trouble ahead of the game.
"It is clear that there was a small minority who were determined to spoil the day for everyone else. Police took a firm, fair and friendly approach allowing those who wanted to enjoy the event in a friendly way to do so."
After the incident, Hull Council leader Carl Minns said: "I am a long-standing football fan but I just can't comprehend this. There is no excuse, it's brought shame on the city."
Trouble also flared in Cleethorpes on Saturday before and after Grimsby Town's pre-season friendly with Sheffield Wednesday.
Police said there had been "pockets of disorder" and made seven arrests for public order offences, possession of an offensive weapon and possession of drugs.