Mueller's MLB playing career was spent with the San Francisco Giants (1996–2000, 2002), Chicago Cubs (2001–2002), Boston Red Sox (2003–2005), and Los Angeles Dodgers (2006).

A switch hitter, he became the only player in major league history to hit one grand slam from both sides of the plate in the same game on July 29, 2003.

Mueller was the starting third baseman for the Red Sox' 2004 World Series championship team that beat the St. Louis Cardinals.

He attended Southwest Missouri State University, was a four-year starter for the Bears baseball team, and in 2004 inducted into the school's athletics hall of fame.

Mueller joined the Los Angeles Dodgers for the 2006 season and was reunited with former Boston teammate Nomar Garciaparra, but played only 32 games before undergoing his third knee surgery, which would prove to be career-ending.

On November 17, 2006, the Dodgers announced that Mueller was retiring as a baseball player, and had been hired as a special assistant to the general manager.

After a month on the job, manager Grady Little announced that the Dodgers would be removing the "interim" tag and that Mueller would remain the teams's hitting coach through the end of the season.

[9] Mueller served as a special assistant to General Manager Ned Colletti through the 2012 season, when he left that position to become a full-time scout.

[13] After being named assistant hitting coach for the 2017 season, he missed part of the first half after taking a personal leave of absence, but returned on June 27.