Thomas attended Brookville High School in Lynchburg, Virginia. He played quarterback, wide receiver, and defensive back for the Bees football team. As a senior, he completed 118 of 204 passes for 1,535 yards and 20 touchdowns and had 842 rushing yards and 11 touchdowns as a quarterback. On defense, he had 80 tackles and four interceptions. He played in the 2009 U.S. Army All-American Bowl.

After being redshirted in 2009, Thomas spent 2010 as the backup quarterback to Tyrod Taylor, appearing in seven games. He completed 12 of 26 passes for 107 yards and 22 rushing yards on six attempts. He also had a two-yard receiving touchdown on his lone reception of the season.

Thomas took over as the starter in 2011. He started all fourteen games, throwing for 3,013 yards and 19 touchdowns while also contributing 469 rushing yards and 11 rushing touchdowns.

In 2012, Thomas completed 220 of 449 passes for 2,976 yards and 18 touchdowns with 16 interceptions. He also rushed for 528 yards and 9 touchdowns. As a senior in 2013, he passed for 2,907 yards with 16 touchdowns and 13 interceptions.

Thomas was drafted by the Arizona Cardinals in the fourth round, 120th overall, of the 2014 NFL Draft. Thomas was the sixth quarterback taken in the draft behind Blake Bortles (3rd, Jacksonville Jaguars), Johnny Manziel (22nd, Cleveland Browns), Teddy Bridgewater (32nd, Minnesota Vikings), Derek Carr (36th, Oakland Raiders), and Jimmy Garoppolo (62nd, New England Patriots). He signed his four-year rookie contract on May 21, 2014.

Thomas made his NFL debut against the Denver Broncos on October 5, 2014, in relief of the injured Drew Stanton. Thomas completed his third career NFL pass for an 81-yard touchdown to Andre Ellington. Thomas became the first NFL quarterback to have his first career completion to go for 80 or more yards since Neil O’Donnell in 1991. Thomas finished the game completing a single pass in eight attempts as the Cardinals were defeated by the Broncos 41–20. After Week 16 and after the Cardinals one sided loss to the Seattle Seahawks, it was announced that the Cardinals would start rookie Thomas over the struggling Ryan Lindley. However, head coach Bruce Arians announced that the team would instead go with Lindley. He was released on September 5, 2015.

Thomas was claimed off waivers by the Miami Dolphins on September 6, 2015. The Dolphins released Thomas on September 11, 2015. He was then re-signed by the Miami Dolphins to their practice squad on September 15, 2015. On December 16, 2015, the Miami Dolphins elevated Thomas from practice squad. The Dolphins waived Thomas on June 16, 2016.

On June 17, 2016, Thomas was claimed off waivers by the New York Giants. On September 3, 2016, he was released by the Giants. The next day, he was signed to the Giants practice squad. Thomas was on and off the Giants’ practice squad throughout the first three months of the season before being released on November 22, 2016, a total of 13 transactions with the team.

Thomas switched his position to tight end and was signed to the Detroit Lions’ practice squad on November 28, 2016.

On November 30, 2016, the Buffalo Bills signed Thomas off the Lions practice squad. Thomas gained significant playing time in 2017 after fellow tight end Charles Clay was sidelined with a knee injury. He caught his first NFL touchdown, a 22-yard pass from former Virginia Tech teammate Tyrod Taylor, during a game against the Tampa Bay Buccaneers on October 22. It was the second time that they connected for a touchdown and the first since college.

On March 21, 2019, Thomas was signed by the Detroit Lions. He was released on September 1, 2019 but was re-signed the following day. He played in all 16 games and started three for the Lions. He finished the season with 16 receptions for 173 receiving yards and one receiving touchdown.

On March 23, 2020, Thomas signed with the Washington Football Team, known as the Redskins at the time. He was placed on the reserve/COVID-19 list for the start of training camp before being activated on August 9, 2020.