Burnett was selected in the eighth round of the 1995 draft by the New York Mets, spending his first three professional seasons in the Mets minor league system. The Mets traded him along with Robert Stratton and Jesus Sanchez for Al Leiter and Ralph Millard.
Burnett would not make his Major League debut until August of 1999, collecting a 4-2 record in his first seven career starts with a 3.48 ERA.
Burnett was sidelined by injuries to start the following season, but joined the team in July and posted a 3-7 record with an unfortunate ERA of 4.79.
On May 12, 2001 Burnett no-hit the San Diego Padres, winning 3-0. His gem was by no means perfect, as he allowed nine walks while striking out seven. In 27 starts that year he compiled an 11-12 record, allowing only 7.5 hits per nine innings, fourth best in the National League.
2002 was Burnett's best season with Florida. He led the NL with five shutouts and with 6.7 hits allowed per nine innings. He struck out 203 in 204.1 innings pitched and posted a 12-9 record with a career best 3.30 ERA.
After a career year in 2002, Burnett was limited by a right elbow ailment to 23 starts over the next two seasons. He came back strong in 2005, posting a 3.44 ERA to go along with his 12-12 record.
He is third on the Marlins All-Time wins list, with a 49-50 record. He posted a 3.73 ERA in 134 games pitched.
Burnett signed as a free agent with the Toronto Blue Jays prior to the 2006 season and recently completed his third season as a New York Yankee.