During Brown's time in Amarillo he also served as the team's pitching coach from 1994 to 1997 and was the club's manager from 1998 to 2000, compiling a 203–77 (.725) record which included winning the Texas–Louisiana League Championship in 1999. He was named the Texas–Louisiana League Manager of the Year in 1999. Since 2001, Brown has worked in the
Seattle Mariners organization. His first job with the Mariners was manager of the club's single-A affiliate, the
San Bernardino Stampede. He helped San Bernardino reach the postseason in 2001 with a 43–27 second-half record, tops in the South Division, but fell in the first round of the playoffs. Brown led club to 77–63 overall record in 2002 and first-place finish in the first half of the season. In 2003 Brown led the Mariners' Class A affiliate, the
Wisconsin Timber Rattlers to a 69–66 record in 2003. Wisconsin earned a playoff berth with a 38–28 first half and finished second in the division. The Timber Rattlers lost in the first round of the post-season. He spent 2004–2005 as manager of the
Inland Empire 66ers. Led them to a 77–63 record and was the only team in Mariners organization to play in the postseason in 2004. In 2006, Brown managed the
San Antonio Missions. Beginning in 2007, Brown managed the Mariners
Triple-A club, the
Tacoma Rainiers. He became the all-time leader in managerial wins in Tacoma franchise history last season when he notched his 376th victory with the Rainiers on May 28, 2012. He led the Rainiers to back-to-back divisional titles in 2009 and 2010, including winning the
Pacific Coast League Championship in 2010. Brown was named the interim manager of the Mariners on August 9, 2010, after the team fired manager
Don Wakamatsu, and by bringing in many players from Tacoma achieved a remarkable initial turnaround. In May 2013, Brown rejoined the Mariners, wearing uniform #52 as extra coach and to fill in as a third base coach when needed, while
Jeff Datz underwent cancer treatment. Brown returned to Tacoma for the 2019 season, after serving in other capacities within Seattle's
farm system. After managing the 2019 Rainiers to 61 wins, he earned his 494th career win with Tacoma. Seattle did not bring back Brown for the 2021 season. Brown was named the manager of the collegiate summer league
Kingsport Axmen in 2021. He was hired to manage the Double-A
Jacksonville Jumbo Shrimp in 2022. On May 22, 2025, Brown was named as the manager for the
Piratas de Campeche of the
Mexican Baseball League, following the firing of
Cory Snyder. He was named the
league's manager of the year after improving the team from ninth place to third place in their division and a spot in the Serie Campeonato. Brown was fired by the Piratas on December 18. In 2026, he became a coach with of the Double-A
Rockey City Trash Pandas.
Managerial record ==Personal==