The first BYU football team in 1896 played the University of Utah (winning 12–4), the Elks, the Crescents, the YMCA of Salt Lake City, the Wheel Club of Denver, and Westminster College; and it ultimately won the championship.

[5] After a 20-year ban on football, the sport was brought back to BYU on an intramural basis in 1919, and intercollegiate games were resumed in 1920 under coach Alvin Twitchell.

The team began to rebuild in the mid-1950s, recruiting University of Rhode Island head coach Hal Kopp to lead the Cougars, who achieved back-to-back winning seasons in 1957 and 1958, led by southpaw quarterback Jared Stephens and nose tackle Gavin Anae.

Edwards and his staff installed a drop-back passing game considered to be an early implementation of the West Coast offense, resulting in Cougar Pete Van Valkenburg as the nation's leading rusher for that year.

The following year, the Cougars struggled to a 5–6 finish, but this would be Edwards' only losing season during his run as BYU coach over the next three decades.

At the end of the season, BYU was voted National Champion after being number one in all four NCAA sanctioned polls AP, Coaches, NFF, and FWAA.

In 1996, BYU won the first ever WAC Championship Game in Las Vegas and earned a bid to play in the Cotton Bowl against Kansas State of the newly formed Big 12 Conference, making it BYU's first ever New Year's Day bowl game, which they won 19–15.

[10] In 1999, BYU left the WAC along with seven other teams to form the Mountain West Conference, with the Cougars winning a share of the inaugural MWC championship.

[13][14][15] BYU originally offered the job to Utah defensive coordinator Kyle Whittingham, who had played for Edwards in the late 1970s.

However, when Whittingham opted instead to become head coach at Utah, the Cougars instead offered the job to BYU defensive coordinator Bronco Mendenhall, who accepted.

But then he just said, ‘But it's a great job.’”[16] Mendenhall led BYU to a bowl game every season he was head coach and saw Top 25 finishes in 2006, 2007, 2008, and 2009.

Weeks later, both leagues reversed course and opted to count games against BYU and the other remaining FBS independent at that time, Army, toward meeting the P5 provision.

In the case of the SEC, this change in policy was driven more by the trend of "Power 5" leagues requiring nine conference games.

[20] In July 2015, the Big Ten announced that games against BYU would count toward the conference's "Power 5" scheduling requirement that takes effect in 2016.

[21] In late 2015, the Big XII Conference added a Power Five non-conference scheduling requirement and stated that BYU would not count toward filling that mandate.

[22] On December 4, 2015, Mendenhall accepted the head coach position with Virginia in the Atlantic Coast Conference (ACC).

BYU spent more than a week courting Navy Midshipmen football head coach Ken Niumatalolo to take over the Cougars program.

After several days, which included a visit to Provo and public remarks about considering the job, Niumatalolo ultimately declined BYU's offer in order to remain with Navy.

Athletics director Tom Holmoe moved on to several other potential candidates and on Dec. 19 introduced Oregon State defensive coordinator and former Cougars fullback Kalani Sitake as BYU's next head coach.

As an independent, BYU was one of just a handful of schools in all of college athletics to generate a profit, enjoying five times the Group of Five average revenue ($13 million).

[34] Official record (including any NCAA imposed vacates and forfeits) against all current Big 12 opponents as of the completion of the 2024 regular season and bowl games.

This change was done at the insistence of new head coach Bronco Mendenhall, who wanted to return the team to the successful traditions of the 1980s.

Edwards had worked with Nike on several occasions since his retirement, and with the legendary coach's weight behind the request, BYU was able to take the field in 2005 in new, traditional uniforms.

On October 13, 2012, BYU debuted a "blackout" jersey for a home game against Oregon State with royal blue accents and black facemasks.

[42] In 2015, renditions of the "throwback" royal blue uniforms appeared, once in the team's Homecoming game against East Carolina, and again against Utah in the Las Vegas Bowl.

With the hiring of Kalani Sitake as head coach at the end of 2015, BYU has seen the gradual return of wearing royal blue combinations.

[44] This last alternate uniform was accompanied by a throwback midfield logo and an endzone paint scheme that matched the field design used by BYU in the 1960s.

A more modern design of the retro combination appeared in a game at the end of the season at San Diego State.

The team wore the gray facemasks several times that season, which was highlighted by the most frequent usage of the royal blue in decades.