Wegerle gained his US citizenship in 1991, after being eligible through his American wife. He made his national team debut on May 30, 1992 against the Republic of Ireland, and would go on to record 41 caps and score seven goals for his adopted country. On January 8, 1994, Wegerle injured his knee and underwent numerous arthroscopic surgeries, but he was able to recover in time to become a key player for the U.S. in the 1994 FIFA World Cup. By 1998, his repeated injuries had hobbled Wegerle. He enjoyed a brief resurgence leading up to the 1998 FIFA World Cup, but never became the key player he had been in 1994. According to former US National Team Manager Steve Sampson, Wegerle came to him and assistant coach Clive Charles between the February 25, 1998 game at Belgium and the March 14, 1998 match against Paraguay in San Diego and said he had personal knowledge of an affair between US Captain John Harkes and Amy Wynalda, the wife of US Striker Eric Wynalda. As a result, Harkes was dropped from the team. The US would go on to finish in last place at the 1998 FIFA World Cup.