After serving 12 years as an assistant coach, including the previous four at California, Kennedy's first collegiate head coaching job came at Centenary. There, he took over a program that had won only 30 games in the previous three seasons. His first team won 10 games but his second improved to a 14-14 overall record and a 9-7 Trans America Athletic Conference mark, its best finish in five years.
Southeastern Louisiana
Southeastern Louisiana hired Kennedy in 1999 and he steadily improved his alma mater, winning 10 games in his first season and doubling that total four seasons later, winning the Southland Conference regular-season championship. His sixth team went 24-9, the most wins in school history, and won both the conference regular-season and tournament titles. The Lions advanced to the NCAA tournamentfor the first time in school history, where it lost to Oklahoma State 63-50. The Louisiana Sports Writers Association, the Louisiana Association of Basketball Coaches, and the National Association of Basketball Coaches selected Kennedy coach of the year in 2004 end 2005. Kennedy resigned from his position at Southeastern Louisiana to become the associate head coach at Miami.
After serving one season as an assistant at Miami, Kennedy was named Murray State's 14th men's basketball coach in 2006, taking over after Mick Cronin departed for Cincinnati. Taking over a team with only one returning starter, he led the Racers to a 16-14 season and second-place finish in the Ohio Valley Conference. His next two squads won 18 and 19 games, again placing second in the conference regular-season standings, and advanced as far as the OVC tournament semifinals. His fourth team at Murray State won more games than any in school history, reaching the second round of the NCAA tournament. The 13th-seeded Racers beat fourth-seed Vanderbilt University 66-65 in the first round in the West Regional at San Jose, California–only the third NCAA Tournament win in school history. They then lost a close second-round contest against fifth-seeded Butler University in the 54-52. During the season, the Racers won a school record 17 games in a row before losing 70-65 at Morehead State University on February 25, 2010. The Racers finished the season with a 31-5 record, including a 17-1 conference mark, and avenged their lone league loss with a 62-51 win over Morehead State in the OVC tournament championship game. Kennedy was named 2010 OVC and National Association of Basketball Coaches coach of the year. In 2010-11, Kennedy's Racers repeated as OVC regular-season champions but fell in the conference tournament semifinals. As OVC regular-season champions, Murray State earned a berth in the National Invitation Tournament where it lost 89-76 at Missouri State to finish with a 23-9 season record. Kennedy was again selected OVC coach of the year.
Texas A&M
hired Kennedy in May 2011. Kennedy previously coached at A&M from 1990-91. Kennedy stated at the press conference that A&M is his destination job and he plans to retire there. He was given the honors of SEC Men's Basketball Coach of the Year in 2016. On October 27, 2011, it was announced that Kennedy had been diagnosed with early-stage Parkinson's disease and would be leaving the team to undergo treatment. Kennedy said he planned to return following treatment and temporarily put Associate Coach Glynn Cyprien in charge of the team. On November 13, 2011, in A&M's second game of the regular season, Kennedy returned to the bench for the Aggies' game against Southern. Kennedy led A&M to its first conference title in 30 years when he shared the SEC crown with Kentucky in 2015-16. The Aggies also made the SEC Tournament final before losing to Kentucky in overtime. For his efforts, Kennedy was given a new 5-year contract. Coach Kennedy's squad that year also orchestrated the largest final-minute come-from-behind victory in college basketball history by overcoming a 12 point deficit in the final 34 seconds of the Second Round of the 2016 NCAA tournament. A&M would tie up the game before finally defeating Northern Iowa in double overtime in order to advance to the Sweet 16 against the University of Oklahoma. Kennedy led A&M to a number five ranking early in the 2017-2018 season and the team finished with 20 regular season wins. The team advanced to the second round of the NCAA tournament to play defending National champion North Carolina, ultimately beating North Carolina by 21 points to advance to the Sweet 16 and a game against Michigan. After a disappointing 2018-19 season, losing four of five starters from the previous season also riddled with injuries and only seven scholarship players, he was fired at the conclusion of the season with two years remaining on his contract.
