Agoos made his debut with the United States national team on January 10, 1988, against Guatemala. His first national team goal came just three days later on January 13, 1988, also against Guatemala. He was the last member to be cut from the U.S. squad for the 1994 FIFA World Cup and he burned his uniform upon hearing the news. He made the squad for the 1998 FIFA World Cup in France but did not play a single minute, in favor of David Regis. In the World Cup in South Korea/Japan at the age of 34, Jeff started the first three games (he scored an own goal to finish the scoring in the surprising win against Portugal) until he suffered a calf injury against Poland. He later missed the rest of the tournament. He was capped a total of 134 times for the U.S. Agoos earned his last cap against Wales on May 26, 2003.