Frei played for Switzerland at Euro 2004 and at the FIFA World Cup 2006 in Germany. He scored two goals in the 2006 FIFA World Cup, one in the match against Togo and a controversial goal against South Korea. Until now he has been capped 58 times for his country (as of June 2008).

Frei is Switzerland's all time top scorer with 35 goals. During Euro 2004, in a group match against England, Frei was caught on camera appearing to spit at Steven Gerrard. Although no action was taken at the time, Frei was later charged and given a provisional 15 day suspension by UEFA. Despite this, he was subsequently cleared of the charge on appeal and atoned by agreeing to take care of a llama.

Within the first half of the opening match of Euro 2008, Frei was injured while captaining the Swiss team and missed the rest of the tournament due to a torn knee ligament in his left knee after a clumsy challenge from Czech defender Zdenek Grygera. However he dutifully sat on the bench with the res