In track and field, Thomas set the school record for shotput and discus with throws of 64 ft 10 in (19.76 m) and 185 ft 7 in (56.57 m). He lettered four times in track and field. He also holds the school indoor record in the shot put (62 ft 11⁄4 in or 18.93 m).
He also excelled at shotput for the Badgers' track and field team. He garnered national recognition for record-breaking performances in shot put and discus throw. He was a 2005 second-team All-Big Ten Conference selection, as he qualified for the 2004 and '05 NCAA Regionals in the shot put and discus throw.
In 2005, Barry Alvarez's final season, he started all 13 games at left tackle and was named a first-team All-American by Pro Football Weekly. He blocked for Brian Calhoun, who had an impressive year, racking up 1,500 rushing yards and 500 receiving yards. Thomas considered declaring for the 2006 NFL Draft, where he was projected among the top 15 picks (and projected as the second offensive lineman behind Virginia prospect D'Brickashaw Ferguson). The Badgers were invited to the Capital One Bowl against Auburn, where they prevailed 24–10. Unfortunately, Thomas tore his ACL playing defensive end because of injuries to other players at the position. The Badgers finished that season 10–3 with a #15 national ranking. Soon after the game, Thomas announced that he would be returning to Wisconsin for his final year.
His senior season in 2006 began with high expectations. As the offensive captain, he started all 13 games and blocked for P. J. Hill, Jr., who racked up over 1,500 yards on the ground. Following the regular season, Thomas won the Outland Trophy as the nation's top interior lineman, and he was recognized as a consensus first-team All-American. Thomas and the Badgers were again invited to the Capital One Bowl, this time against Arkansas. The Badgers prevailed 17–14 and finished the season 12–1, a school record for wins in a single season.
The Cleveland Browns drafted Thomas in the first round of the 2007 NFL Draft (3rd overall) to fill a dire need on the team's offensive line. The Thomas pick ended much speculation that the Browns would choose other players including former Notre DameQBBrady Quinn with the 3rd overall pick in the draft. Quinn, who was widely expected to be a top 10 pick, waited patiently until he left for the private suite of Commissioner Goodell. Quinn was later picked 22nd after the Browns traded up. Instead of attending the 2007 draft festivities in New York, Thomas chose to go fishing on Lake Michigan with his father, father-in-law and Joe Panos, who was also a standout offensive lineman at Wisconsin and former Brookfield resident. Thomas discovered he was drafted by the Cleveland Browns via cell phone.
Thomas signed a six-year contract worth $43 million, $23 million guaranteed, including a voidable year, with the Browns. Thomas won the starting left tackle job, with previous Browns left tackle Kevin Shaffer moving to right tackle. He made his NFL debut versus the Pittsburgh Steelers in week 1 and played every offensive snap for the Browns in 2007. Thomas quickly became one of the top-performing members of the 2007 draft class and was named the NFL's Rookie of the Month for November. Thomas was selected to the 2008 Pro Bowl, replacing Jason Peters of the Buffalo Bills.
Thomas has made the AFCPro Bowl roster all seven of his seasons in the NFL
On August 22, 2011 Thomas and the Cleveland Browns agreed to a seven-year $84 million extension with almost $44 million guaranteed.
On December 27, 2011, Thomas was named to his fifth straight Pro Bowl since the Cleveland Browns drafted him. Since 1970, Thomas and Richmond Webb of the Miami Dolphins are the only NFL offensive linemen to make the Pro Bowl in each of their first five seasons. Thomas and Pro Football Hall of Fame running back Jim Brown are the only Browns players ever to be selected to the Pro Bowl for the first five seasons of their careers. Hall of Fame running back Leroy Kelly was the last Browns player to earn five or more consecutive invitations to the Pro Bowl.
On December 26, 2012, Thomas was named to his sixth straight Pro Bowl. Thomas joins a short list of only 15 players who have made the Pro Bowl in each of their first six seasons in NFL history.
On December 27, 2013, Joe Thomas was voted to his seventh straight Pro Bowl selection. Thomas joins Hall of Famer Jim Brown as the only two Browns to make the Pro Bowl in their first seven seasons. Thomas on making his 7th straight Pro Bowl became one of only 11 players in NFL history to make it their first seven seasons. The list of other players who have done it and gone on to make the Hall of Fame includes Dick Butkus, Joe Greene, Franco Harris, Merlin Olsen, Mel Renfro, Barry Sanders, Lawrence Taylor and Derrick Thomas.