He was named the team's "Captain for Life" by then-head coach Steve Sampson before having that title stripped ahead of the 1998 World Cup.

Following his retirement, he served as a color commentator for ESPN's coverage of MLS and U.S. international matches, including the 2010 FIFA World Cup.

[9] Harkes played for University of Virginia where he was named 1st team All-American in 1986 and 1987, and was the Hermann Award winner in 1987, as the best player in US colleges.

MLS had signed numerous prominent U.S. players and eventually allocated them throughout the league's teams in order to create an initial equitable distribution of talent.

The United States side was routed 1–5 by Czechoslovakia, but were respectable losing 0–1 to host nation and eventual semi-finalist Italy, and 1–2 to Austria.

Despite losing all three matches, many players from the 1990 squad, including Harkes, Ramos, Meola, Marcelo Balboa formed the core of the U.S. national team for most of the decade and played an important role in the development of MLS.

U.S. fared better as the host nation in the 1994 World Cup, upsetting Colombia 2–1 in a group stage match to advance to the Round of 16.

Harkes contributed to the Andrés Escobar own goal which arguably led to the Colombian defender's shooting death weeks later.

[17] Harkes delivered a cross from the left aimed at Earnie Stewart, which Escobar attempted to clear, but instead sent the ball past his goalkeeper.

However, Harkes missed the Round of 16 match against Brazil after receiving his second yellow card of the group stage against Romania, earning a one-match suspension.

In Copa América 1995, Harkes led the United States, a guest team at the tournament, to a 3–0 upset of defending champion Argentina and a semi-final finish.

However, Sampson controversially left Harkes off the World Cup squad, citing "leadership issues", although the decision was never fully explained at the time.

[21] Harkes was called up to the national team again by his former college coach, Bruce Arena in 1999, and helped the United States win the bronze medal in the Confederations Cup that year.

In August 2015, the formation of FC Cincinnati, a new franchise in the then-third-division United Soccer League, was announced, with Harkes as the team's first head coach.

[23] From outside the club, the dismissal was seen as a surprise; reports later emerged of a 2016–17 offseason that was "unstructured and somewhat chaotic behind the scenes", according to The Cincinnati Enquirer's Pat Brennan.

[24] In August 2018, Harkes was named as the first head coach of Greenville Triumph, a new club set to join USL League One in 2019.

In the 2020 season, the Triumph finished first in the standings and won the playoffs, and Harkes was named the USL League One Coach of the Year.

Despite intense criticism from the media and subsequent failure in the World Cup, Sampson remained silent regarding the true reason for Harkes' dismissal from the team out of respect for the privacy of those involved.