He signed with the Phillies and began his professional career with the Batavia Muckdogs, where he was honored as a member of the New York–Penn League's All-Star team.

Brooks's performance caught the eye of the Pittsburgh Pirates, who acquired him in a deadline deal for closer Mike Williams.

After spending most of 2004 at Triple-A, Brooks made his major league debut on August 27, 2004, and went on to appear in eleven games with the Pirates.

He pitched well in relief, striking out 17 batters in 161⁄3 innings and surrendering only a .175 batting average to opposing hitters, but his final season totals were distorted by a poor performance in an emergency start.

On November 8, 2006, Brooks signed a minor league contract with the San Diego Padres and became a free agent after the season.