Unable to find playing time in Europe, Hejduk returned to the United States and Major League Soccer for the 2003 season, where he was allocated to Columbus Crew.
Hejduk immediately found a spot as team leader right back for the Crew, and went on to start 23 games for the team that season, assisting on four goals.
He played a similar role at right back and right midfield in 2004, starting 19 games and scoring two goals for a club that won the MLS Supporters Shield.
On January 25, 2007, the Columbus Crew announced that they had signed Hejduk to a two-year contract extension, keeping him with the Crew through the 2008 MLS season.
On November 23, 2008, Hejduk headed home a pass from Guillermo Barros Schelotto to provide the final goal in a 3–1 victory securing the Crew's first MLS Cup.

After the 2010 MLS season Columbus declined Hejduk's contract option and Hejduk elected to participate in the 2010 MLS Re-Entry Draft.
On December 15, 2010 Hejduk was selected by Sporting Kansas City in Stage 2 of the Re-Entry draft, and subsequently traded to Los Angeles Galaxy later the same day.
He played six first-team games and another five games with the Galaxy reserve team.
At season's end, Los Angeles declined his 2012 contract option and Hejduk entered the 2011 MLS Re-Entry Draft.
After no other club selected him, Los Angeles exercised its option to retain his MLS rights.
However, on January 30, 2012 the club announced that it was unable to come to terms with Hejduk and that he would not play for Galaxy in 2012.

Rather than having microfracture surgery on his ankle and additional surgery to repair a broken wrist, Hejduk officially announced his retirement from professional soccer on April 19, 2012, opting to accept a position in the Crew front office.
Unable to find playing time in Europe, Hejduk returned to the United States and Major League Soccer for the 2003 season, where he was allocated to Columbus Crew. Hejduk immediately found a spot as team leader right back for the Crew, and went on to start 23 games for the team that season, assisting on four goals. He played a similar role at right back and right midfield in 2004, starting 19 games and scoring two goals for a club that won the MLS Supporters Shield. On January 25, 2007, the Columbus Crew announced that they had signed Hejduk to a two-year contract extension, keeping him with the Crew through the 2008 MLS season. On November 23, 2008, Hejduk headed home a pass from Guillermo Barros Schelotto to provide the final goal in a 3–1 victory securing the Crew's first MLS Cup.
After the 2010 MLS season Columbus declined Hejduk's contract option and Hejduk elected to participate in the 2010 MLS Re-Entry Draft. On December 15, 2010 Hejduk was selected by Sporting Kansas City in Stage 2 of the Re-Entry draft, and subsequently traded to Los Angeles Galaxy later the same day. He played six first-team games and another five games with the Galaxy reserve team. At season's end, Los Angeles declined his 2012 contract option and Hejduk entered the 2011 MLS Re-Entry Draft. After no other club selected him, Los Angeles exercised its option to retain his MLS rights. However, on January 30, 2012 the club announced that it was unable to come to terms with Hejduk and that he would not play for Galaxy in 2012.
Rather than having microfracture surgery on his ankle and additional surgery to repair a broken wrist, Hejduk officially announced his retirement from professional soccer on April 19, 2012, opting to accept a position in the Crew front office.
Frankie Hejduk