Thomas was drafted by the Baltimore Ravens in the sixth round (186th overall) in the 2000 NFL Draft. Competing with Peter Boulware and Michael McCrary for playing time, Thomas made only 89 tackles in his first three years. He was inactive for 12 games in his rookie season, but played in all 16 games in the 2001 season, starting two at defensive end. In 2002, he started 12 games at defensive end, recording two interceptions as well as 15 special teams tackles. In 2003, Thomas was recognized for his special teams play and was selected to his first Pro Bowl. That year, he registered 34 tackles, 8 passes defended, 4 sacks, and a forced fumble. He was placed on injured reserve by the Ravens on December 17, but still led the team with 23 special teams tackles.