Mauer was selected by the Minnesota Twins in the 23rd round (677th overall pick) of the 2001 Major League Baseball Draft, the same draft in which they selected his younger brother, Joe Mauer (who would go on to have a 15-year career with the team before being elected to the Baseball Hall of Fame in 2024), with the first overall pick.

In Mauer's two seasons at the helm, the GCL Twins went 69-42, finishing in second and first, respectively, in the Gulf Coast League's Southern division.

On October 21, 2009, he was named manager of the Fort Myers Miracle following Jeff Smith's promotion to the double A New Britain Rock Cats.

The Mauers have a third brother, Billy, who signed with the Twins as an undrafted free agent in 2003, and pitched in the organization for three seasons before chronic shoulder problems forced him to retire from the game.

He ended his minor league career with a 3-4 record and 3.66 earned run average in 43 games.