In 2000, Payne began her women's basketball coaching career at Gonzaga under Kelly Graves. The team improved from five wins in 2000–01 to 28 wins in the 2004-05 season, including a perfect record in West Coast Conference play. Payne helped recruit guard Shannon Mathews, who would become the first All-American in program history.
In 2005, Payne became an assistant coach at Boise State under Gordy Presnell. During her time as assistant, Boise State won Western Athletic Conference titles two of her three years and made the NCAA Tournament. Boise State finished 24-8 twice in a row, including a perfect 14-0 home record in the 2007-08 season.
In 2009, JR Payne got her first head coaching position, at Southern Utah. In five seasons, Payne led Southern Utah to a record 23-win season, Big Sky Conference regular season co-championship, and first-ever postseason appearance in program history in the 2014 Women's National Invitation Tournament.
On March 28, 2016, Payne became head coach at Colorado. The eighth head coach in program history, Payne replaced Linda Lappe, who was fired after only managing only a career 33-57 record in Pac-12 play. JR Payne inherited a program that only finished 7-23 in Lappe's final season. JR Payne inherited a program that had a lack of player talent. The Buffs were only 14-58 in the last four years of Linda Lappe's coaching tenure in Pac-12 play, despite having the program's All-Time assists leader in each year during that time frame. Colorado finished the 2018-19 season with a 2-16 Pac-12 record. In it 45 years history, it marked the fifth time that the Buffs failed to win at least three conference games. Payne's 2018-19 Colorado team began Pac-12 conference play 0-11, the worst start to conference play in program history. The 102-43 loss at Oregon was the Buffs' worst loss since 1984 and it was the 4th worst loss in program history. Prior to the start of the 2019-20 season, the Buffs was anticipated to continue to struggle, and were picked to finish last place in the Pac-12 Women's Basketball Coaches poll by fellow Pac-12 coaches. Yet, Payne and her staff invested in completely remaking the culture of the Colorado Buffs women's basketball team and the team bought in. The Buffs finally turned the corner from the program's struggles to play at a competitive level within the Pac-12 conference and jumped straight to playing competitively against the top nationally ranked teams within the conference. The Buffs put a scare into #6 ranked Stanford, taking the Cardinal to overtime. Colorado put a scare into #8 ranked UCLA, having a chance to tie the game on the last possession. Colorado, once again, played competitively against Stanford, but lost on a half court buzzer beater on a crucial turnover. Colorado upset #11th ranked Arizona on Feb 23, 2020 to get their fifth Pac-12 win on the season. It marked the first win over a ranked opponent since 2016 and stopped a 32 games losing streak against ranked opponents.
Personal life
She is married to assistant coach Toriano Towns and they have three children together: Aliyah, Jordan, and Jaxton.
