Freeze attended Senatobia High School and the University of Southern Mississippi, from which he graduated in 1992 with a Bachelor of Science degree in mathematics and a minor in coaching and sports administration.

In 1992, Freeze joined the staff at Briarcrest Christian School in Memphis, Tennessee, as the football team’s offensive coordinator and defensive backs coach. Freeze also served as dean of students. In 1995, he was promoted to head coach. Freeze ran the no-huddle spread offense and led his team to the state championship twice, in 2002 and 2004, and the regional championship each year from 1995 to 1998 and in 2001 and 2002. He received Region 8-AA Coach of the Year honors five times and Associated Press Coach of the Year honors six times. In ten years at Briarcrest, Freeze was 94–30 as head coach (.785 winning percentage) and 126–37 overall. Freeze was depicted in the book and motion picture The Blind Side, about one of his former players, current free agent offensive tackle Michael Oher.

In 2005, the University of Mississippi hired Freeze as an assistant athletic director for football external affairs. The following season, he became the tight ends coach and recruiting coordinator, positions he held through 2007. After that season, he replaced head coach Ed Orgeron on an interim basis before the hiring of Houston Nutt. Freeze interviewed for the offensive coordinator position with Nutt, a position that eventually went to Kent Austin.

In January 2008, Lambuth University, a member of the National Association of Intercollegiate Athletics (NAIA), named Freeze its head coach. In 2008, he led Lambuth to an 8–4 record and a first round loss in the NAIA playoffs, marking their first appearance in the playoffs since 2004 under then head coach Vic Wallace. He was considered for the University of Tennessee at Chattanooga’s head coaching position following the 2008 season, but remained at Lambuth University for another season and compiled a 20–5 overall record, and defeating opponents 41–17 on average. In 2009, he led the Eagles to their best regular season record in school history with an unblemished 11–0 mark. Lambuth advanced to the second round of the NAIA playoffs for first time in 11 years—having won one game before suffering elimination to finish 12–1 as the sixth-ranked team in the NAIA.

In 2010, he joined the staff of head coach Steve Roberts at Arkansas State as offensive coordinator, joining the program after spending less than two months, during the 2009-2010 offseason, as offensive coordinator at San Jose State University.

In 2011, his only season as head coach at Arkansas State, he led the Red Wolves to a 10–2 record and their first Sun Belt Conference title since 2005. The Red Wolves’ offense averaged 447.8 ypg (28th nationally, 1st in Sun Belt Conference) including 293.6 ypg passing and 154.2 ypg rushing. Freeze left Arkansas State before Arkansas State’s post-season appearance in the GoDaddy.com Bowl.

On December 5, 2011, Freeze was announced as the 37th head coach of the University of Mississippi. During the press conference to introduce Freeze as the head coach, he stated that he wanted to “retire at Ole Miss.” He was signed to a four-year contract with an annual salary of $1.5 million plus incentives up to $2.5 million.

In his first season at Ole Miss, Freeze led the Rebels to a 6–6 record in the regular season, making Ole Miss bowl eligible for the first time since 2009 with a 41–24 victory over Mississippi State in the Egg Bowl. His Rebels accepted a bid to play in the BBVA Compass Bowl in Birmingham, Alabama, on January 5, 2013. They beat the University of Pittsburgh 38–17 to finish 7–6.

During Freeze’s third season at Ole Miss, he led the Rebels to a 7–0 start, the program’s best start since the Johnny Vaught era. By October, they had risen as high as third in the nation, their highest ranking at that late stage in the season in almost half a century. They ultimately finished 9–3, only the third time since Vaught’s tenure that Ole Miss has won that many games in the regular season. That netted them an appearance in the 2014 Peach Bowl: their first major bowl appearance since the 1970 Sugar Bowl, and the biggest since Vaught’s tenure.

On September 19, 2015, Freeze’s Rebels beat Alabama, 43–37, in Tuscaloosa, Alabama, making Freeze only the third head coach, along with Les Miles and Steve Spurrier, to defeat a Nick Saban-coached team in back-to-back years (Michigan’s Lloyd Carr beat Saban’s Michigan State Spartans in three consecutive years, ’96–’98). The victory catapulted the Rebels to No. 3 in the AP rankings. They went on to tally their second straight nine-win season, and garnered a berth in the 2016 Sugar Bowl, where they won 48–20 over Oklahoma State. They finished ninth in the AP Poll and 10th in the Coaches’ Poll—their first top-10 finishes in a final poll since 1969. It was also only the Rebels’ third 10-win season since the Vaught era.

In January 2016, the NCAA charged Ole Miss with numerous recruiting violations. An investigation turned up evidence that Ole Miss employees and boosters arranged numerous “impermissible benefits” for players, such as car loans and cash. At least one recruit was suspected of getting help on his college entrance exam.

Following his dismissal from Ole Miss in 2017, some former students alleged that Freeze had engaged in inappropriate conduct with female students while at Briarcrest. Freeze has denied the allegations. Briarcrest officials said they were unaware of any sexual improprieties committed by Freeze during his tenure.

On July 13, 2017, Freeze’s predecessor, Houston Nutt, sued Ole Miss for defamation, contending that Freeze and school officials falsely blamed him for the violations. As part of discovery for the lawsuit, Nutt’s attorneys filed a Freedom of Information Act request for calls Freeze made on his university-issued cell phone during January 2016. Nutt’s attorneys contended that Freeze and others at Ole Miss leaked information to the press as part of an effort to smear their client.

On October 11, 2018, Freeze was offered a job as offensive coordinator of the Arizona Hotshots of the Alliance of American Football league; he turned it down.

Freeze was named head coach of the Liberty Flames football team on December 7, 2018.

In February 2019, the NCAA punished the Ole Miss football team for the recruiting and academic violations committed under both Nutt and Freeze. The punishments included a two-year postseason ban, three years of probation, and a four-year ban on some scholarships. As well, the NCAA forced Ole Miss to vacate 33 wins from 2010 to 2016. As a result, 27 of Freeze’s wins were stripped from the books; only the 2015 season was unaffected. His record at Ole Miss is now officially 12–15; it was 39–25 on the field.

On December 10, 2019, Freeze signed a 5-year extension with Liberty.