Wuerffel was a first-team All-American in 1995, and a consensus first-team All-American in 1996. He received the Sammy Baugh Trophy in 1995, the Davey O'Brien Award in 1995 and 1996, and the Johnny Unitas Golden Arm Award in 1996, and was named the Quarterback of the Year by the Touchdown Club of Columbus in 1996. Wuerffel declined to be included on Playboy magazine's All-America team as well as its Scholar-Athlete of the Year award, saying, "That's not the type of person I am or would like to portray myself as." His Gators teammates picked him as the squad's most valuable player in 1995 and 1996; his coaches chose him as one of the Gators' team captains. He was later named to The Gainesville Sun's Florida Gators Team of the Century in 1999, was chosen by the Sun as the number one player in the first 100 years of Gators football, and was listed as a member of the Florida Gators 100th Anniversary Team in 2006.
He is one of only two Heisman Trophy winners to also receive the Draddy Trophy, which is presented annually by the National Football Foundation and the College Football Hall of Fame to the nation's top football scholar-athlete. Wuerffel was also a first-team Academic All-American in 1995 and 1996.
He finished his Gator career by completing 708 of 1,170 passes for 10,875 yards with 114 touchdown passes, the best in SEC history and second-most in major college history. His career pass efficiency rating of 163.56 was the best in major college history and his percentage of passes which went for a touchdown (9.74) ranked first in collegiate history. In 1995, his efficiency rating of 178.4 set a single-season collegiate record. During his Heisman-winning season of 1996, he completed 207 of 360 passes for 3,625 yards (an SEC record at the time) for 39 touchdowns (leading the nation) and his efficiency rating of 170.6 made him the first quarterback to ever post a rating of 170 or better in back-to-back years.