After his career in the NFL, Phillips became a graduate assistant on the Kentucky football team. In 1990, he was promoted to assistant recruiting coordinator and in 1991 to wide receivers coach. In 1997, he was hired as wide receivers coach at the University of Cincinnati. Following two seasons in Cincinnati, Phillips made coaching stops at Minnesota, Notre Dame, and South Carolina. Phillips succeeded Urban Meyer as wide receivers coach at Notre Dame. When Rich Brooks was hired as head football coach at Kentucky in late 2002, Phillips returned to his alma mater to serve as recruiting coordinator and wide receivers coach. With the departure of Ron Hudson late in the 2004 season, he was named offensive coordinator of the Wildcats. Phillips helped to rejuvenate Kentucky's offensive scheme. Under Phillips' balanced offense, André Woodson established himself as one of the top quarterbacks in the country. In his first full season as offensive coordinator, Kentucky finished with an 8–5 record and defeated Clemson in the 2006 Music City Bowl. In 2007, Kentucky finished the season with another 8–5 record, defeating Florida State in the 2007 Music City Bowl. Winning the Music City Bowl for the second year in a row was the first time the Wildcats had won two consecutive bowls in over 50 years. The Wildcats finished in the top 15 nationally in points scored per game and averaged 460 yards of offense. In 2008 the Wildcats finished 7–6 with a victory over East Carolina in the Liberty Bowl. In January 2008, Phillips was named as Brooks' successor, and his title was changed to "head coach of the offense". He was named head coach of the Wildcats on January 4, 2010 after Brooks' retirement. Phillips was the second African-American head football coach in the SEC, after former Mississippi State coach Sylvester Croom. He was also the third African-American head coach of a major sport at Kentucky; the first was Bernadette Maddox, who coached the women's basketball team from 1995 to 2003, and the second was Tubby Smith, who coached men's basketball from 1997 to 2007. In 2011, he led the Wildcats' to a season-ending 10–7 victory over Tennessee, their first over the Volunteers since 1984, ended the longest current losing streak against an annual opponent in FBS at 26. Kentucky athletic director Mitch Barnhart announced on November 4, 2012 that Phillips would not return as coach in 2013 after a 1–9 start to the season. Barnhart did say that Phillips would coach the remaining games and finish out the year on the sidelines for the Wildcats. On December 3, 2012, Phillips was hired by the University of Florida as wide receivers coach and recruiting coordinator. In April 2014, Florida suspended Phillips for impermissible conduct with a recruit; Phillips resigned in June 2014. In February 2015, the NCAA ruled that Phillips committed a Level II violation that "was not inadvertent and provided more than a minimal recruiting advantage." The NCAA did not penalize Florida. On January 29, 2015, the Cleveland Browns hired Phillips as wide receivers coach under Mike Pettine. Phillips was not retained for the next season, when Hue Jackson replaced Pettine as head coach. On June 29, 2016, Ohio State hired Phillips as a Quality Control Assistant under head coach Urban Meyer.
Personal life
Joe Phillips, Jr. was given his nickname "Joker" by his grandfather to distinguish him from his father, also named Joe. He was married to Leslie Stamatis, associate professor of kinesiology at Georgetown College in Kentucky, from 1999 through 2017 when they divorced.