Thomas erupted onto the scene in the 2013 season. He scored his first and second career touchdowns in the season opener against the Baltimore Ravens on September 5, 2013, having a five catch, 110-yard, two-touchdown breakout performance. Both of Thomas's touchdowns came from quarterback Peyton Manning. He followed up this performance in Week 2 with a six-catch, 47-yard performance that ended with a game-sealing touchdown against the New York Giants. In Week 3, he continued his scoring streak against the Oakland Raiders with three receptions for 37 yards and a touchdown. Thomas played his best game of the season in Week 5, catching nine passes for 122 yards and two touchdowns in a 51–48 shootout win against the Dallas Cowboys. On October 13, he had four receptions for 22 yards and a touchdown against the Jacksonville Jaguars. On October 20, he had five receptions for 41 yards and a touchdown against the Indianapolis Colts. On November 10, 2013, he had three receptions for 96 yards and a touchdown against the San Diego Chargers. In Week 16, in a win over the Houston Texans, Thomas caught a touchdown from Peyton Manning, which was his 51st touchdown pass of the season, which set a single season record.