The travelling supporters had set up shop in a square in the Old Town section of the Czech capital, continuing a rowdy display after reportedly being warned, in English, that they faced police action.
After that warning was ignored, the authorities arrived, armed and wearing riot gear. The visiting fans responded by throwing bottles at the police, who in turn launched stun grenades at them.
Around 12 fans were pinned into a corner and forced to the floor. Reports suggest there have been 20 arrests, and two people injured. The extent of those injuries has not been made known.
There were concerns before the game that the late kick off, 8:45pm local time, with the fixture being played on a Friday and Prague’s reputation as a party town would potentially lead to problems with England’s travelling contingent.
The Three Lions have had problems in recent years across Europe, with similar incidents seen in Amsterdam, Porto and Dortmund.
This time 3,800 fans bought tickets for the game, but more are thought to have made the trip.
There has been no statement as to whether or not those arrested had tickets to the game, which the Czech Republic won 2-1.
Those that did make it to the stadium witnessed Harry Kane give England the lead from the penalty spot after only five minutes.
The skipper made it 20 goals as captain and 27 overall when he converted from 12 yards after Raheem Sterling was fouled.
Kane’s tally as captain is tied with Alan Shearer and Brian Robson for goals scored wearing the armband, only Vivian Woodward, who scored 23 has more than the trio.
England were soon pegged back as Jakub Brabec bundled home after a Jakub Jankto free-kick unnerved Gareth Southgate’s defence.
As the game entered its dying minutes, Czech forward Zdenek Ondrasek popped up with a winner to give the Three Lions the first blemish on their Euro 2020 qualifying record.
The focus before this week’s Euro 2020 qualifiers was on potential trouble in Bulgaria’s stadium.
England forward Tammy Abraham said his team would walk off if there was any racial abuse from fans in that game.
Abraham’s words upset Bulgarian FA president Borislav Mihalylov, and Southgate said he understood why, adding that England had problems of their own.