The following rule changes were made by the NCAA Football Rules Committee for the 2013 season:
Players who intentionally deliver a blow above the shoulders of a defenseless player (targeting) will now be automatically ejected from the game in addition to the 15-yard penalty assessed. If the ejection occurs in the first half, it is for the remainder of the game. If the ejection occurs in the second half or in overtime, it is for the remainder of the game plus the first half of the next scheduled game. The ejection penalty is automatically reviewed to determine if the hit was intentional, however the yardage penalty is not reviewable (this was changed in the 2014 season to overturn the yardage penalty if the ejection was overturned).
Blocking below the waist is now legal if done from the front side of the defender anywhere on the field, while blocks below the waist delivered from the side or back are fouls, simplifying rule changes from the 2011 and 2012 seasons.
In the final minute of each half, if the clock is stopped solely for an injured player, there will be an option for a 10-second runoff before the ball is put in play to cut down on teams faking injuries to stop the clock. If the clock is stopped for another reason (first down, incomplete pass, etc.) or if players from both teams are injured on the same play no runoff will occur.
Establishing three seconds as the minimum time required to be on the game clock to spike the ball to stop the clock and get an additional play. If one or two seconds remain on the game clock when the ball is spiked, the half or game will end.
Permitting the use of electronic equipment (such as wireless headsets) for game officials to communicate with each other.
Two players at the same position on the same team may not wear the same uniform number (example, two quarterbacks on the same team cannot wear #12).
Players that change numbers during a game must report to the referee, who will announce it via wireless microphone. Failure to report is an unsportsmanlike conduct penalty (15 yards).
Instant replay will be permitted to adjust the game clock at the end of each quarter. Previously, instant replay could only adjust the game clock at the end of each half.
Permitting the Big 12 Conference to experiment with an eighth official during conference games, positioned in the offensive backfield opposite the Referee (similar to the positioning of the umpire in the NFL) to assist in detecting infractions (such as holding, chop blocks, blindside hits on the quarterback, etc.) on the offensive line as well as spotting the ball and monitoring substitutions. This official will be referred to as an "alternate referee" and wear an "A" on the back of the uniform. Use of eight-man officiating crews was expanded to all FBS conferences in the 2014 season.
A rule that would have required the colors of uniform jerseys and pants to contrast to the field was recommended by the Rules Committee but was denied by the Playing Rules Oversight Panel. This rule was proposed to prevent teams (such as Boise State) from wearing uniforms that matched the color of their field. Another recommended rule would have switched the side of the field on which the line-to-gain and down markers are displayed in each half but was also denied.
The NCAA Legislative Council also approved a new rule that allows any FBS team with a 6–6 record entering a conference championship game to be bowl-eligible regardless of the result of the title game. Previously, such teams (for example, Georgia Tech last season and UCLA in 2011) had to seek an NCAA waiver if they lost in their conference championship.
The Western Athletic Conference dropped football as a sport after the 2012-13 season, becoming the first conference since the Big West Conference after the 2000-01 season to do so, as most of its football-playing members announced their departure for other conferences, and the 2 staying for 2013-14 temporarily became football independents.
May 14 – The University of Hawaiʻi at Mānoa announced that effective July 1, all of the school's men's sports teams, including football, would use the nickname of Rainbow Warriors, a combination of the school's historic name of "Rainbows" and the "Warriors" nickname used by some teams since 2000. This reversed a plan announced by UH in February 2013, under which all men's teams would use "Warriors", previously used by football, men's golf, and men's volleyball. UH had allowed men's teams to choose their own nicknames in 2000, which resulted in the baseball team using "Rainbows", the three aforementioned teams using "Warriors", and other men's teams using "Rainbow Warriors". The change did not affect UH women's sports, which continue to be known as Rainbow Wahine.
October 10 – Minnesota and its head coach Jerry Kill jointly announced that Kill would take an indefinite leave of absence, effective immediately, to focus on treatment and management of his epilepsy. Kill had missed the second half of the Golden Gophers' win over Western Illinois on September 14 due to a seizure, and was unable to travel with the team to Michigan on October 5 due to his condition. Minnesota named defensive coordinator Tracy Claeys as interim head coach; Kill returned to the team for the Northwestern game on October 19, but remained in the press box, allowing Claeys to direct the team from the sidelines until resuming on-field duties in the second half of the Texas Bowl.