Thibault left the Lakers for the Chicago Bulls in 1982 and remained with the latter organization through the 1985-86 season, serving as an assistant coach and director of scouting; under Thibault, the team drafted shooting guard Michael Jordan and power forward Charles Oakley and acquired John Paxson, each of whom would contribute to the Bulls' earning six league championships between 1991 and 1999.

In 1989, Thibault began an eight-year stint as general manager and head coach of the Omaha Racers of the Continental Basketball Association, in which capacity he led the team to the league playoffs in each season; his team claimed the 1993 championship and once more reached the league finals one year thence.

Contemporaneously, Thibault worked for USA Basketball as a coach for the United States national team, leading the national side to a gold medal at the 1993 FIBA World Championship qualifying tournament and a silver medal at the 1995 Pan American Games.

Thibault returned to the NBA during the league's 1997-98 season and, through 2003, served as a scout and assistant coach for each of the Atlanta Hawks, New York Knicks, and Seattle SuperSonics; most prominently, Thibault spent four seasons with the Milwaukee Bucks as an advisor and assistant to George Karl.

[6][7] On July 7, 2018, when the Mystics beat the Los Angeles Sparks, Thibault became the first WNBA coach to reach 300 wins.

He guided the Mystics to the team's first-ever championship in the 2019 WNBA Finals, as they defeated the Connecticut Sun.

Newcomers Sue Bird, Candace Parker and Diana Taurasi picked up the slack, but it was a team in transition.

As an additional challenge, some members of the squad were unable to join the team for practices due to WNBA commitments.