Brown signed with the Bulls in 1995, and he provided valuable energy and aggressiveness off the bench during the Bulls' second "three-peat" (1996–1998). In the clinching game of the 1996 NBA Finals against the Seattle SuperSonics, Brown was the first player to get on the floor with Michael Jordan to celebrate. A fan favorite, Brown was also one of the few veteran players who stayed with the Bulls after the 1998-99lockout. With the absence of Michael Jordan, Scottie Pippen, and Dennis Rodman, he became a full-time starter and averaged 8.8 points, 3.8 assists, and 3.4 rebounds (all career highs) during the remainder of the 1998-99 season. After one more season in Chicago, Brown played briefly for the Boston Celtics and the Phoenix Suns, and he retired from the NBA in 2003 with 3,148 career points and 1,420 career assists.
Brown was later an assistant coach with the Kings. In 2009, Brown began an online auction in order to sell his three NBA championship rings after filing for Chapter 7 bankruptcy.
In July 2009, Brown was hired by the Bulls as their director of player development. The next year, he was named special assistant to the general manager. In 2013, he was promoted to assistant general manager.