Meier received FIFA appointments and refereed in the Swiss top division until he reached the mandatory retirement age for each. He now appears as an expert summariser on the German television channel ZDF during World Cups and European Championships. He also owns a brand of household appliances in Würenlos, Switzerland.
At the 1998 World Cup, Meier refereed the heated USA-Iran match. It was an emotional match because of the political situation, and supposedly a hard one to referee because of this, in what was one of his earliest games as a World Cup referee.
During a qualification match for Euro 2004 between Romania and Denmark, he awarded a controversial penalty kick for Denmark. Meier also let play go on for longer than the amount of time added on originally recommended by the fourth official, making it seven minutes instead of four. Denmark equalized during the added time to eliminate Romania. After several Romanian newspapers published his email address after the game, Meier received 14,000 e-mails. Several petitions were sent to UEFA, but they were disregarded.
In the Euro 2004 quarter-final between England and Portugal at Lisbon, with the score at 1–1, he disallowed a goal by Sol Campbell in the 89th minute due to a perceived foul by John Terry on the Portuguese goalkeeper Ricardo Pereira. There was some disquiet before the game amongst the English fans because England had defeated Switzerland 3-0 in the group stages, eliminating them. The match ended in a draw, and Portugal proceeded to the next stage following a penalty shootout and reached the final (where they lost to Greece).
UEFA backed Meier, but English fans and media contested the accuracy of his decision — condemning Meier. English tabloids dubbed him "Urs hole", "idiot ref" and "Swiss banker".
After Meier's personal details were published by British tabloid newspapers, Meier received more than 16,000 abusive e-mails, and death threats. Reporters of The Sun even travelled to Switzerland and placed an oversized English flag on a field near his home. As a result, he was placed under police protection.