Hejduk attended San Dieguito High School where he played on the boys' soccer team. He was also a member of the powerhouse La Jolla Nomads Soccer Club which won the California state youth championship in 1989, 1990 and 1991. After high school, Hejduk attended UCLA. He spent three seasons, 1992 to 1994, as a defender on the UCLA Bruins soccer team. While a defender, he was the second leading scorer in 1994 with six goals. He was also named an NCAA second-team All-American his junior year.
In February 1996, the Tampa Bay Mutiny drafted Hejduk in the seventh round (67th overall) of the 1996 MLS Inaugural Player Draft. Hejduk went on to play the league's first three seasons. However, commitments to the Olympic team limited him to only eight games as a rookie. In 1997, Hejduk established himself on the Mutiny defense, playing 22 games and registering 1 goal and 6 assists. He did much of the same in 1998, registering 3 goals and 1 assist with the team over 18 games while missing significant time while playing in the 1998 FIFA World Cup.