In 2011, Allen served as the assistant head coach at Arkansas State, his first position with a Division I FBS program. The head coach during this time was Hugh Freeze, who Allen had previously coached with at Lambuth University. After the end of the regular season, Allen followed Freeze to Ole Miss after Freeze was hired to be the head coach of the Rebels. In his sole season with the Red Wolves, they went 10–2.
Ole Miss (2012–2014)
From 2012 to 2014, Allen spent three seasons as the linebackers coach and special teams coordinator at Ole Miss under head coach Hugh Freeze. During his time in Oxford, the Rebels went 24–15 and consistently ranked near the top of the FBS in terms of tackles for loss and sacks. Prior to his arrival, Ole Miss had ranked last in the SEC in total defense.
South Florida (2015)
On December 17, 2014, Allen was named defensive coordinator at South Florida under third-year head coach Willie Taggart. In his lone season in Tampa, Allen's defensive unit ranked first in the American Athletic Conference in scoring defense at just 19.6 points per conference game. His efforts also saw the team's defense rank high nationally, tying for 13th nationally in tackles for loss, 14th in interceptions, 24th in takeaways, 26th in sacks, 31st in rushing defense, 34th in passing efficiency defense, and 35th in scoring defense. Allen was considered a candidate for the defensive coordinator position at Auburn following then-defensive coordinator Will Muschamp's departure in December 2015, but the vacant position was ultimately filled by Kevin Steele.
Indiana (2016–present)
Allen was hired on January 15, 2016 to serve as defensive coordinator on head coach Kevin Wilson's staff at Indiana. In replacing previous defensive coordinator Brian Knorr, Allen took over a defense that ranked #120 in the FBS in total defense and #106 in opponent points scored. After just one season, Allen engineered one of the top defensive turnarounds in the country with the team improving in every major statistical category against a schedule featuring four top-10 opponents, a program first. The Hoosiers were the most improved team nationally in total defense and passing defense, the sixth-most improved in third-down defense and the ninth-most improved in points per game allowed. On December 1, 2016, Indiana athletic director Fred Glass named Allen head coach after Wilson's sudden resignation, forcing Allen to make his coaching debut during the team's final game of the season at the 2016 Foster Farms Bowl. His contract guaranteed him $1.795 million annually — $500,000 per year in base pay, plus $1.295 million per year in outside, marketing, and promotional income. This made Tom Allen the lowest paid head coach in the Big Ten, although various bonuses could take his total compensation above $3 million. Allen quickly elevated Indiana's recruiting posture. During his first two seasons as head coach, a school-record number of players earned conference honors and a school-record were drafted or invited to NFL camps. The 2019 signing class was the highest rated in program history, besting his previous top-ranked class of 2018, and the two classes combined constituting 80 of the team's 115-man roster. In 2019, Allen's third season, he led Indiana to its first 7-2 start since 1993, the last season Indiana won eight games. That season Indiana earned a #24 ranking in the Associated Press and #25 ranking in the coaches poll, the team's first top 25 ranking in football since 1994. His 17 wins over his first three seasons were the most for an Indiana coach in the post-World War II era. Indiana finished the regular season with an 8-4 record, its first eight-win since 1993, and its 5-4 Big Ten record its first winning conference record since 1993. Following the regular season, Allen and the school agreed to a new seven-year contract with an average annual compensation of $3.9 million.
