He started coaching immediately after he retired from playing rugby in 1988, where he became the head coach of Auch until 1995. During his time as coach at the club, he led the team to 4 Top 16 rounds, 3 of which came in consecutive years. In 1995, he arrived at Colomiers, where in just his second season in charge, he led the team to the Quarter-finals of the 1996–97 French Rugby Union Championship. During the 1997–98 season, he led the team to the Semi-final of the French Rugby Union Championship, but narrowly lost to Perpignan 15–12. However, he did oversee Colomiers first ever trophy wear, when they won the 1997–98 European Challenge Cup. In 1999, Brunel took the team one step forwards, leading them to the 1999 Heineken Cup Final, only to lose to Ulster 21–6.