The 1999 NCAA Division I-A football season saw Florida State named national champions, defeating Virginia Tech in the BCS Sugar Bowl.

Florida State became the first team in history to start out preseason No. 1 and remain there through the entire season. Their 12–0 season gave them 109 victories in the '90s, the most for any decade. Virginia Tech also had a remarkable season behind freshman quarterback Michael Vick, who was being touted as college football's best player.

Vick was outshone in the national championship game by Florida State wide receiver Peter Warrick. Warrick had early problems with the law, charged with a misdemeanor he sat out two games early in the season. But he scored three touchdowns in the title game, earning MVP honors.

The BCS adopted a new rule after the previous season, nicknamed the "Kansas State Rule," which stated that any team ranked in the top four in the final BCS poll is assured of an invitation to a BCS bowl game.

Many teams faced debacles. East Carolina faced Hurricane Floyd, and in that same week, faced the No. 9 Miami Hurricanes. The Pirates were down, 23–3, but scored 24 unanswered points to win the football game, 27–23.

Kansas State finished 6th in the BCS standings but again received no BCS bowl invitation, this time being passed over in favor of Michigan (ranked eighth). Kansas State's predicament demonstrated early on the problem of trying to balance historic bowl ties and creating a system which gives top bowl bids to the most deserving teams. In addition, for a second straight season, a team from outside the BCS Automatic Qualifying conferences (Marshall) went undefeated but did not receive a bid to a BCS bowl game, which illustrated the problem of BCS Non-Automatic Qualifying conference teams being shut out of the BCS bowls.

Rule changes The NCAA Rules Committee adopted the following changes for the 1999 season: Holding penalties committed behind the line of scrimmage will be enforced from the previous spot, modifying a 1991 rule that penalized holding (as well as illegal use of hands and clipping) committed behind the scrimmage line from the spot of the foul. The penalty for intentional grounding was changed from a five-yard penalty from the spot of the foul plus loss-of-down to simply a loss-of-down at the spot of the foul. Bandannas that are visible are considered illegal equipment. Offensive teams may not break a huddle with 12 or more players. Continuing action dead-ball fouls against both teams are disregarded, however any disqualified players must leave the game.

Conference and program changes Two teams upgraded from Division I-AA, thus increasing the number of Division I-A schools from 112 to 114.

The Mountain West Conference was formed prior to the season by eight former members of the Western Athletic Conference. Arkansas State joined the Big West Conference as its seventh member after three seasons as an independent. Alabama–Birmingham joined the Conference USA after playing three seasons as an I-A Independent. Two schools made the move up to Division I-A football this season: the University at Buffalo and Middle Tennessee State University.

Conference changes School 1998 Conference 1999 Conference Air Force Falcons WAC Mountain West Alabama–Birmingham Blazers I-A Independent Conference USA Arkansas State Indians I-A Independent Big West Buffalo Bulls I-AA Independent MAC (I-A) BYU Cougars WAC Mountain West Colorado State Rams WAC Mountain West Middle Tennessee Blue Raiders Ohio Valley (I-AA) I-A Independent New Mexico Lobos WAC Mountain West San Diego State Aztecs WAC Mountain West UNLV Rebels WAC Mountain West Utah Utes WAC Mountain West Wyoming Cowboys WAC Mountain West

Program changes Two programs, each playing as independents, changed their names prior to the season: After Northeast Louisiana University changed its name to the University of Louisiana at Monroe, the Northeast Louisiana Indians became the Louisiana–Monroe Indians. Similarly, after the University of Southwestern Louisiana changed its name to the University of Louisiana at Lafayette, the Southwestern Louisiana Ragin' Cajuns became the Louisiana–Lafayette Ragin' Cajuns.

Regular season

August–September In the preseason AP Poll, No. 1 Florida State was followed by No. 2 Tennessee, the team which had defeated them in last year's championship game. The top five were rounded out by No. 3 Penn State, No. 4 Arizona, and No. 5 Florida.

August 28: No. 1 Florida State beat Louisiana Tech 41–7, and No. 3 Penn State blasted No. 4 Arizona by the same 41–7 score in the Pigskin Classic. The other highly ranked teams had not begun their seasons, and the next AP Poll featured No. 1 Florida State, No. 2 Penn State, No. 3 Tennessee, No. 4 Florida, and No. 5 Nebraska (who moved up from sixth place).

September 4: No. 1 Florida State was idle. No. 2 Penn State posted another blowout win, 70–24 over Akron. No. 3 Tennessee began their schedule with a 42–17 defeat of Wyoming, No. 4 Florida beat Western Michigan 55–26, and No. 5 Nebraska won 42–7 at Iowa. The top five remained the same in the next poll.

September 11: No. 1 Florida State got past No. 10 Georgia Tech by a 41–35 score. No. 2 Penn State had an even closer call, needing a late field goal and a block of a potential game-tying kick with time running out to preserve a 20–17 win over rival Pittsburgh. No. 3 Tennessee was idle. No. 4 Florida beat Central Florida 58–27, and No. 5 Nebraska shut out California 45–0. The next poll featured No. 1 Florida State, No. 2 Tennessee, and No. 3 Penn State, with Florida and Nebraska tied at No. 4.

September 18: No. 1 Florida State beat No. 20 North Carolina State 42–11. No. 2 Tennessee visited No. 4 Florida, whom they had defeated in 1998 after several frustrating losses earlier in the decade. This time, the Gators went back on top in a 23–21 squeaker. No. 3 Penn State edged past No. 8 Miami as the Nittany Lions followed a crucial fourth-down stop with a 79-yard touchdown pass to win 27–23. No. 4 Nebraska dropped out of the top five after struggling to beat Southern Mississippi 20–13. A tie-breaking safety proved to be the key play in No. 6 Michigan's 18–13 win at Syracuse, while No. 7 Texas A&M overwhelmed Tulsa 62–13. The next poll featured No. 1 Florida State, No. 2 Penn State, No. 3 Florida, No. 4 Michigan, and No. 5 Texas A&M.

September 25: No. 1 Florida State visited North Carolina for a 42–10 victory, No. 2 Penn State defeated Indiana 45–24, and No. 3 Florida won 38–10 at Kentucky. No. 4 Michigan held eventual Heisman Trophy winner Ron Dayne without a single rushing yard in the second half of the Wolverines' 21–16 victory at No. 20 Wisconsin. No. 5 Texas A&M beat Southern Mississippi 23–6, and the top five remained the same in the next poll.

October October 2: No. 1 Florida State beat Duke 51–23. No. 2 Penn State was idle. No. 3 Florida hosted No. 21 Alabama for a thriller in which the Crimson Tide's Shaun Alexander ran for four touchdowns, including game-tying scores both at the end of regulation and in overtime. Alabama missed the extra point on the latter touchdown, but an offsides penalty gave their kicker a second chance, and this time he converted the point-after for a 40-39 finish which was Florida's first loss at home in five years. No. 4 Michigan defeated No. 11 Purdue 38–12, but No. 5 Texas A&M was upset 21–19 by Texas Tech. No. 6 Nebraska won 38–14 over Oklahoma State, and No. 8 Virginia Tech pulled off a 31–7 victory at No. 24 Virginia. The next poll featured No. 1 Florida State, No. 2 Penn State, No. 3 Michigan, No. 4 Nebraska, and No. 5 Virginia Tech.

October 9: No. 1 Florida State hosted No. 19 Miami and won 31–21, while No. 2 Penn State visited Iowa for a 31–7 victory. No. 3 Michigan fell 34–31 to No. 11 Michigan State as the Spartans' Bill Burke and Plaxico Burress set school records for passing and receiving yards. No. 4 Nebraska defeated Iowa State 49–14, and No. 5 Virginia Tech won 58–20 at Rutgers. The next poll featured No. 1 Florida State, No. 2 Penn State, No. 3 Nebraska, No. 4 Virginia Tech, and No. 5 Michigan State.

October 16: No. 1 Florida State beat Wake Forest 33–10, and No. 2 Penn State defeated No. 18 Ohio State 23–10. No. 3 Nebraska was idle. No. 4 Virginia Tech overwhelmed No. 16 Syracuse 62–0; not only did the Hokies' offense put on a show, but the defense also returned two fumbles and an interception for touchdowns. No. 5 Michigan State lost 52–28 at No. 20 Purdue. No. 6 Tennessee was idle, but nevertheless moved back into the top five: No. 1 Florida State, No. 2 Penn State, No. 3 Nebraska, No. 4 Virginia Tech, and No. 5 Tennessee.

October 23: Clemson coach Tommy Bowden nearly pulled off an upset against his father Bobby's top-ranked Florida State team, but the Seminoles escaped with a 17–14 victory. No. 2 Penn State looked ineffective on offense, but the Nittany Lions converted three turnovers into touchdowns in a 31–25 win at No. 16 Purdue which moved coach Joe Paterno into third place on the all-time wins list. No. 3 Nebraska also struggled to hold onto the ball, losing three fumbles (including a crucial one at their opponent's 2-yard line) in a 24–20 loss at No. 18 Texas. No. 4 Virginia Tech was idle. No. 5 Tennessee visited No. 10 Alabama for a 21–7 win, and idle No. 6 Florida returned to the top five: No. 1 Florida State, No. 2 Penn State, No. 3 Virginia Tech, No. 4 Tennessee, and No. 5 Florida. The first BCS standings, released after this weekend's games, had the same top four but placed Kansas State at No. 5.

October 30: No. 1 Florida State won 35–10 at Virginia, No. 2 Penn State went to Illinois for a 27–7 victory, No. 3 Virginia Tech was a 30–17 winner at Pittsburgh, No. 4 Tennessee beat South Carolina 30–7, and No. 5 Florida defeated No. 10 Georgia 30–14. The top five remained the same in the AP Poll, and Florida's big victory was sufficient to move the Gators from sixth to fourth place in the BCS standings.

November November 6: No. 1 Florida State was idle. Unranked Minnesota completed a 4th-and-16 pass to set up a game-winning field goal and stun No. 2 Penn State 24–23; after their hot start, the Nittany Lions would lose all of their remaining regular-season games by a touchdown or less. Another thriller took place in Morgantown, where No. 3 Virginia Tech led West Virginia 19–7 with five minutes left but then allowed two Mountaineers touchdowns in quick succession. In a last-ditch effort, Michael Vick led the Hokies on a 58-yard drive resulting in a field goal which put them back on top 22–20 as time expired. No. 4 Tennessee beat No. 24 Notre Dame 38–14, No. 5 Florida escaped Vanderbilt 13–6, and No. 6 Kansas State held off Colorado 20–14. The next AP Poll featured No. 1 Florida State, No. 2 Virginia Tech, No. 3 Tennessee, No. 4 Florida, and No. 5 Kansas State; the BCS standings had Tennessee second and Virginia Tech third.

November 13: No. 1 Florida State defeated Maryland 49–10. No. 2 Virginia Tech beat No. 19 Miami 43–10. No. 3 Tennessee blew a fourth-quarter lead to Arkansas and lost 28–24, while No. 4 Florida won 20–3 at South Carolina to clinch a spot in the SEC Championship Game. No. 5 Kansas State fell 41–15 at No. 7 Nebraska. No. 9 Wisconsin breezed past Iowa 41–3 to win the Big Ten title and a spot in the Rose Bowl. The next AP Poll featured No. 1 Florida State, No. 2 Virginia Tech, No. 3 Florida, No. 4 Nebraska, and No. 5 Wisconsin, while the BCS standings had Nebraska third, Florida fourth, and Tennessee fifth.