In 1999, Quinlan played third base for the Low-A Boise Hawks making the Short-Season All-Star team and being named the Northwest League's MVP. He batted.322 with 9 home runs and 77 RBI. In, he was promoted to High-A Lake Elsinore and moved to first base; he hit.317 with 85 RBI. Quinlan was promoted to Double-A Arkansas for and after a solid year, began with Triple-A Salt Lake as an outfielder. 2002 was a career year for Quinlan. He spent the entire year with Triple-A Salt Lake and hit.333, posting career-highs in home runs, RBI, hits, and triples. He was named Pacific Coast League Rookie of the Year, PCL MVP, and Anaheim Angels Minor League Player of the Year. He was also named a Triple-A All-Star, PCL All-Star, and one of Baseball America's 1st team minor league All-Stars. Quinlan started in the minors with Triple-A Salt Lake, but after batting.310, he was called up to the majors where he spent the rest of the year. He began with Triple-A again, but was called up to the majors after 27 games.
Major leagues
Quinlan made his major league debut on July 28,, and hit.287 for the rest of the year. After starting 2004 in Triple-A, he was called up the first week in May. He had a 21-game hit streak in 2004 from July 7 to August 10 which is the longest by an Angels rookie in club history, and was the longest by any rookie in the majors since Ichiro Suzuki in. On August 17, he was placed on the 15-day disabled list with a torn oblique muscle, causing him to miss the rest of the year. For the season, Quinlan batted.344, including.407 in July, with 5 home runs and 23 RBI. In, Quinlan, playing part-time, saw his batting average drop over 100 points to.231 and missed time with a bulging disk and inflamed shoulder. He rebounded in with a.321 average and saw a career-high in playing time with 234 at-bats in 86 games. Quinlan signed a two-year, $1.8 million contract before the season avoiding arbitration, but his batting average slumped again to.247. In, he played in 68 games mostly at third base and slightly improved his average to.262. After the 2009 baseball season Quinlan filed for free agency for the first time in his career. On February 11, 2010, Quinlan agreed to a minor league contract to return to the Angels. He was added to the Major League roster at the end of spring training. On September 7, 2010, Quinlan was released by the Angels. Quinlan signed a minor league contract with the Philadelphia Phillies with an invitation to spring training for the 2011 season. On March 11, 2011, the Phillies reassigned Quinlan and his agent asked for his release, which the Phillies granted.
After playing
In May 2011, Quinlan became a volunteer coach and hitting instructor for the University of Minnesota, his alma mater, through at least the 2011-12 season. Since 2013, Quinlan has been the owner of multiple chiropractic franchises. Tom and Robb Quinlan are part of the ownership group for the St. Croix River Hounds, a collegiate summer baseball team scheduled to begin playing in the Northwoods League with the 2021 baseball season.