He played in Major League Baseball (MLB) for the San Diego Padres, Minnesota Twins and New York Mets.

[2] Stauffer played for the Keene Swamp Bats of the New England Collegiate Baseball League in the summer of 2001, where he set an NECBL record with a 7–0 win/loss mark.

[4][5][6] Stauffer was selected in the first round by the San Diego Padres as the fourth overall pick of the June 2003 draft.

He was quickly promoted through Double-A and reached the Triple-A Portland Beavers in June, posting a 3.54 ERA in 14 starts with the club.

He was called up to the Padres for a single appearance on August 21, 2006, in order to temporarily fill a spot in a pitching rotation hampered by injuries.

The surgery and rehab cost him the entire 2008 season, and Stauffer began 2009 with the Double-A San Antonio Missions after a month of extended spring training to build arm strength.

He got his first opportunity to start on May 9, taking the place of Kevin Correia, but Stauffer required an emergency appendectomy on May 11, sidelining him for nearly two months.

[9] Stauffer was again the planned Opening Day starter, but he suffered an elbow strain in spring training and went on the disabled list.

After the season, the Padres did not tender an offer to Stauffer, and he elected for free agency after clearing waivers.

Stauffer signed a new one-year, $1.6 million deal with San Diego on December 2, 2013, avoiding arbitration.

[15] Stauffer again primarily worked out of the pen as long reliever, making three starts in late May and early June after Robbie Erlin went to the disabled list.

[19] On July 14, 2015, Stauffer signed with the Sugar Land Skeeters of the Atlantic League of Professional Baseball.