He attended San Diego State University from 1987 to 1989 where he played for the Aztecs men's soccer team, scoring 34 goals and assisting on 25 others during his three seasons. His freshman year, SDSU went to the NCAA Men's Soccer Championship game where it lost to the Bruce Murray led Clemson Tigers. While at SDSU, he also played two seasons with the local semi-pro San Diego Nomads of the Western Soccer Alliance. In 1988, he played a single game and in 1989, he played 5 games with the Nomads.

Wynalda came back to the States in 1996, signing with Major League Soccer (MLS). As part of the process of creating the new league, known players were distributed throughout the league's new teams (except for the Dallas Burn, which alone amongst all MLS sides never received a US National Team allocation from the 1994 World Cup era). The league allocated Wynalda to the San Jose Clash. On April 6, 1996 Wynalda scored the first goal in league history in its inaugural game as the Clash beat D.C. United 1-0. He was named U.S. Soccer Athlete of the Year.
After the 1998 World Cup, Wynalda began seeking a move back to Europe. While he had publicly declared that he would never return to Germany, including turning down a January 1998 offer from Kaiserslautern, he now began putting out feelers there. When no German teams expressed an interest in Wynalda, he then sought a move to England. In December, he had a trial with Charlton Athletic, but the team did not offer Wynalda a contract and Wynalda returned to the Clash. 
Wynalda was loaned out to Club León in Mexico in 1999. He tore both the ACL and medial meniscus on his left knee while with Leon which put him out of action for several months.
After missing the first eleven games of the 1999 season, the Clash traded Wynalda to the Miami Fusion. On July 8, 2000, the Fusion turned around and traded Wynalda to the New England Revolution for Ivan McKinley after Wynalda failed to improve the Fusion's offensive output. On May 3, 2001, the Revs sent him to the Chicago Fire for John Wolyniec, where he finished his MLS career, ending up with a total of 34 MLS goals (plus two in the playoffs). In 2002, Wynalda joined the Los Angeles Galaxy, announcing that he planned to retire with the team. However, he left the Galaxy during the team's pre-season tour of Chile in order to pursue an offer to play professionally in China. When that offer fell through, he returned to the Galaxy only to leave it for the Charleston Battery of the USL First Division after feuding with the MLS front office about his salary. MLS was offering to pay Wynalda $43,000 for the 2002 season which Wynalda considered much too low.
As the Battery had offered him $75,000, Wynalda joined that team only to tear his anterier cruciate ligament in a pre-season match.
He elected to retire from professional soccer and became a broadcast announcer.
Later that year, Wynalda played in his first World Cup gaining the dubious honor of becoming the first U.S. player to be ejected from a World Cup game. That came when Czechoslovakian midfielder Lubomir Moravcik baited Wynalda in front of a referee. Wynalda, showing his immaturity, retaliated and was shown red. 
In the 1994 FIFA World Cup, Eric scored on a free kick from 20 yards as the United States tied Switzerland. He also played in Copa America 1995, where he was named to the all-tournament team after scoring against Chile and Argentina.
In 1998, Wynalda participated in his third World Cup, one of four U.S. players (Tab Ramos, Tony Meola and Marcelo Balboa) to earn that honor. Claudio Reyna and Kasey Keller have since gone on to be named to a record four World Cup rosters.
Wynalda retired from the US National Team as its all-time leading scorer with 34 goals in 106 appearances. He was the sole owner of the record until 2007, when Landon Donovan tied the record with a penalty kick goal against Mexico in the 2007 CONCACAF Gold Cup final. He was named the Honda US Player of the Decade for the 1990s and elected to the National Soccer Hall of Fame in 2004.
, and in 2007 he agreed a short-term playing contract with the team during the last few matches of their season.
. On May 1, 2008, he signed a formal season-long agreement to play the entire campaign with the Brigade as a full member of the 2008 playing squad. 
He has also continued to play with an over-30s amateur team in Los Angeles, Hollywood United, alongside former U.S. internationals Alexi Lalas and John Harkes, former French international Frank Leboeuf, former Welsh international player Vinnie Jones, and actor Anthony La Paglia.
United plays in the Los Angeles Olympic Soccer League.
After a number of controversies, he left ESPN prior to the 2008 season, a year before his contract was due to expire.
In 2006, Eric was appointed a Goodwill Ambassador of the Intergovernmental Institution for the use of Micro-algae Spirulina Against Malnutrition, IIMSAM.