As a senior in 1995, he was a unanimous first-team All-American, the Big 12 Conference Defensive Player of the Year, and a finalist for the Butkus Award.

Thomas is one of 5 Red Raiders to be named a Unanimous All-American along with Mark Bounds, Byron Hanspard, Michael Crabtree, and Jace Amaro.

[14] He impressed the Dolphins' coaching staff during training camp and quickly rose up the depth chart to compete for the job as the starting middle linebacker against Jack Del Rio.

Head coach Jimmy Johnson officially named Thomas the starting middle linebacker to begin the regular season.

On October 13, 1996, Thomas recorded 11 combined tackles, a sack, and made his first career interception during a 21–7 win at the Buffalo Bills in Week 7.

Thomas made his first career interception off a pass by Bills' quarterback Jim Kelly, that was originally intended for tight end Lonnie Johnson, and returned it for an 11-yard gain in the first quarter.

[19] On November 17, 1996, Thomas made eight combined tackles and returned an interception for his first career touchdown in the Dolphins' 23–20 win against the Houston Oilers in Week 12.

Thomas intercepted a pass by Oilers' quarterback Chris Chandler, that was intended for tight end Frank Wycheck, and returned it for a 26-yard touchdown in the fourth quarter.

In Week 14, Thomas recorded six combined tackles and made a season-high two interceptions in the Dolphins' 27–17 win at the Oakland Raiders.

The following week, he made ten combined tackles as the Dolphins' lost to the Denver Broncos in the AFC Divisional Round 38–3.

[32] Thomas's $6.5 million in salary and bonus made him the Dolphins highest paid player, surpassing Dan Marino.

[33] Head coach Jimmy Johnson retained Thomas, Robert Jones, and Derrick Rodgers as the starting linebackers in 1999.

On January 9, 2000, Thomas recorded nine combined tackles and a sack during a 20–17 victory at the Seattle Seahawks in the AFC Wildcard Game.

The following week, he made ten combined tackles as the Dolphins lost 62–7 at the Jacksonville Jaguars in the AFC Divisional Round.

Wannstedt opted to retain Thomas as the starting middle linebacker, alongside Robert Jones and Derrick Rodgers.

[39] He started in the Miami Dolphins' season-opener at the Tennessee Titans and recorded nine combined tackles, deflected two passes, and returned an interception for a touchdown in their 31–23 victory.

[40] Thomas intercepted a pass by Titans backup quarterback Neil O'Donnell, that was intended for tight end Erron Kinney, and returned it for a 34-yard touchdown in the fourth quarter.

[40] Thomas finished the 2001 season with 154 combined tackles (94 solo), three sacks, two pass deflections, two interceptions, and a touchdown in 15 games and 15 starts.

[42] Head coach Dave Wannstedt chose to rest Thomas during the Dolphins' Week 17 win against the Buffalo Bills as they had already clinched a playoff berth.

On January 13, 2002, Thomas recorded 22 combined tackles (14 solo) during the Dolphins' 20–3 loss against the Baltimore Ravens in the AFC Wildcard Game.

[43] On December 29, 2002, Thomas collected a season-high 16 combined tackles (11 solo) in the Dolphins' 27–24 loss at the New England Patriots in Week 17.

[48] On November 27, 2003, Thomas made six combined tackles, a pass deflection, a sack, and an interception during a 40–21 victory at the Dallas Cowboys in Week 13.

Thomas intercepted a pass by Cowboys' quarterback Quincy Carter, that was intended for wide receiver Terry Glenn, in the fourth quarter.

In Week 3, he collected a season-high 16 combined tackles (nine solo), broke up a pass, and made a sack during a 27–24 win against the Carolina Panthers.

Thomas finished his tenth season in 2005 with 158 combined tackles (104 solo), three pass deflections, two sacks, and two interceptions in 14 games and 14 starts.

[63] He started in the Miami Dolphins' season-opener at the Washington Redskins and collected a season-high 13 combined tackles (nine solo) and made one sack in their 16–13 loss.

[64] On December 4, 2007, the Miami Dolphins officially placed Thomas on injured reserve after he missed five games (Weeks 8–13) due to his repeated migraine headaches.

[67] On February 14, 2008, the Miami Dolphins released Thomas after announcing that he no longer fit into their long-term plans and his contract was terminated.

[69] The signing of Thomas surprised media and observers, considering that he didn't have the previous experience or the size to play in the Cowboys 3-4 defense.

[76] On May 18, 2010, the Dolphins signed Thomas to a one-day ceremonial contract, officially worth $1, in order to retire as a member of the team.