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. Since 2007, Brown has managed the Seattle Mariners Triple-A club, the Tacoma Rainiers. The Holdenville, Oklahoma native 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 vs. Tucson. He led the Rainiers to back-to-back divisional titles in 2009 and 2010, including winning the PCL Championship in 2010. Brown was named the interim manager of the Seattle 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 is the all-time winningest manager in team history. The name of Brown's wife is Cindy, and the couple have a home in Amarillo, Texas.