After graduating from college, Clifford became a teacher at Woodland High School in Maine. He also gained his first coaching experience at the school, serving as their head coach for two seasons while leading them to two tournaments. He then served as an assistant coach at St. Anselm's College, Fairfield University, Boston University and Siena College. In 1995, he assumed the head coaching duties at Adelphi University and coached for four seasons under Keith Dickson, leading their team to four appearances in the NCAA Division II Tournament, an 86–36 record and four consecutive 20-win seasons; he was the first coach in the school's history with back-to-back 20-plus win seasons. Clifford became an NBA assistant coach with the New York Knicks and Houston Rockets under Jeff Van Gundy and quickly developed a reputation as a defensive expert. He then was an assistant for Stan Van Gundy with the Orlando Magic. He considers both the Van Gundy brothers as mentors. He reached the NBA Playoffs in each of his five seasons with Orlando, appearing in the NBA Finals in 2009. Clifford then joined the Los Angeles Lakers in 2012–13 as an assistant.
Charlotte Bobcats/Hornets
On May 29, 2013, Clifford was hired by the Charlotte Bobcats to be their head coach. Clifford implemented a defensive mentality in Charlotte during his first year as head coach turning the Charlotte Bobcats into a top five defensive team when in the years prior to his tenure they ranked near the bottom of the NBA in that category. He led the Bobcats to the 2014 NBA playoffs in his first year as head coach, during which he coached the Bobcats to a 43–39 record. The two years prior to him joining the Bobcats only had a combined total of 28 wins. He was named Eastern Conference Coach of the Month for April 2014 after he led the Bobcats to a 7–1 record leading to the playoffs. He finished fourth in Coach of the Year voting in his first year. On December 6, 2017, it was announced that Clifford would not coach indefinitely to deal with his health issue. On January 11, 2018, the Hornets announced that Clifford was medically cleared to return to coaching after a 21-game absence after dealing with sleep deprivation. After the 2017–18 regular season, he was fired as head coach on April 13, 2018, after five seasons coaching the team to a 196–214 record total.
Orlando Magic
On May 30, 2018, Clifford was named the head coach of the Orlando Magic. The Magic started the 2018–19 season by splitting their first 24 games before falling 11 games under.500 after a 126–117 loss to the Oklahoma City Thunder. Despite the dismal start, Clifford led the Magic on a dramatic turnaround. On April 7, 2019, Orlando defeated the Boston Celtics 116–108 to clinch their first playoff berth since the 2011–12 season. The win also clinched the Magic's first Southeast Division title since the 2009–10 season. This was the Magic's first playoff appearance since trading Dwight Howard to the Los Angeles Lakers in 2012, ending the longest playoff drought in franchise history.
