Thomas attended Central Coosa High School in Rockford, Alabama, and was a letterman in football and basketball.

In basketball, as a senior, he led his team to the State Title and was named the Alabama Class 4A Player of the Year.

Thomas was named a Freshman All-American by the Sporting News in 1996, leading the Golden Eagles to an 8–3 record and a share of the Conference USA title.

Southern Miss finished 9–3 in Thomas's sophomore season, en route to a Conference USA Championship and a victory in the Liberty Bowl.

Thomas earned third-team All-American and Defensive Player of the Year honors as a senior, in addition to being named the MVP of the 1999 Liberty Bowl.

In 2005, with Boulware relegated to situational pass-rush duty, Thomas was named the starting outside linebacker, where he accumulated 84 total tackles and 9 sacks.

Thomas earned his second Pro Bowl bid in 2006 as part of a Ravens defense that finished first in the league en route to a 13–3 record.

He was a first-team All-Pro after setting a career-high with 106 tackles and 11 sacks, as well as notching 1 interception, 1 safety, 7 passes defensed, and 1 fumble recovery returned 57 yards for a touchdown.

After the move, Patriots head coach Bill Belichick told Thomas that he had "backed up the Brink's truck" to pay him.

[3] Thomas played mainly at inside linebacker in the Patriots' 3-4 defense in 2007, rotating with veterans Tedy Bruschi and Junior Seau.