Brady was previously the head men's basketball coach at Louisiana State University in Baton Rouge, Louisiana. On February 8, 2008, LSU dismissed Brady, and named his assistant coach, Butch Pierre, the interim head coach for the remainder of the season. On March 21, 2008 Coach John Brady was named the 15th head basketball coach at Arkansas State University
In 2000 the Tigers broke through, posting a 28-6 record and an NCAA Tournament Sweet 16 appearance. However, due to the loss of Stromile Swift and Jabari Smith to the 2000 NBA Draft, the Tigers could not carry their momentum to the next year, going 13-16 in 2001.
Brady's team entered the 2005-06 season unranked, but were coming off a solid season in which they went 20-10 and made the NCAA Tournament. Led by Glen "Big Baby" Davis and Tyrus Thomas, the Tigers won their first outright SEC regular season championship since 1985, and earned a #4 seed in the NCAA Tournament. After wins over Iona and Texas A&M, LSU defeated the #1 seed Duke and #2 seed Texas to make it to their first Final Four since 1986. Set at the RCA Dome in Indianapolis, Indiana, the 2006 Final Four was the first since 1980 to feature no #1 seeds (LSU, #2 UCLA, #3 Florida and #11 George Mason). Facing the #2 seed Bruins in the national semifinals, the Tigers were unable to solve UCLA's defense, losing 59-45, dropping LSU to 0-6 all-time in the men's Final Four (and 0-10 in all Final Four games, including an 0-4 mark in the women's Final Four). Despite the loss, the 2005-06 season will be remembered as one of the most successful in LSU men's basketball history. John Brady was fired in the middle of his 11th season as LSU's head basketball coach and just two seasons after the Tigers' latest Final Four appearance.
In 10 seasons at LSU, Brady compiled a 184-126 record, including two SEC Western division titles and four NCAA tournament appearances.
On February 08, 2008, Brady was fired from LSU. Earlier news reports stated that he would coach the Tennessee game on February 9, but LSU officials stated that his termination was immediate. Brady's assistant coach, Butch Pierre, took over as the interim head coach.