Now he'll head the Brewers' entire Minor League system.
"It's a really exciting opportunity," Flanagan said. "I know many of the people involved, I know what everybody is about, and in my time with David I've gotten to know how important player development is from his perspective. I can't wait to get going in the new role."
Among his duties in the previous post, Flanagan worked with former farm director Reid Nichols in matters of personnel and staffing in the Minor League chain. Nichols was dismissed from the job in October as part of Stearns' reorganization.
"All along, we said we wanted to find the person who would most effectively lead our player development group, and at the end of the day, we're very confident that Tom's that guy," Stearns said. "Familiarity can help in that position, but more than anything, Tom came in and presented a clear and focused strategy and vision for what he believes in player development, the communication he believes is important. He persuaded us that he has the ability to be a very successful farm director."
In addition to the 100-150 players in the Minor League system, depending on the time of year, Flanagan will also oversee about 50 staff, some of whom also report to the Brewers' medical department but play a vital role in player development.
Flanagan's aim, he said, is "making sure you have everyone pulling in the same direction and putting the same policies in place."
"Establishing processes, that's one of the No. 1 objectives in the next couple of months," he said. "I want to meet with all of our rovers and our managers and put these processes down on paper in a clear fashion so guys know what they need to do moving forward. I want us to be in unison when we bring these ideas to the players in the spring."
Asked to identify his core principles of player development, Flanagan said, "The biggest thing is we need to have our philosophy and our game plan, so to speak, for both players and staff in place, so everybody can get feedback on where they stand and where we see them going forward. I don't want to sound like we haven't done that in the past, but I want to really reinforce it. You hate to use the cliché of the 'Brewers Way,' but the things that are most important to us, you want to make the staff and the players aware of those."
For the time being, Flanagan's former duties will be absorbed by director of baseball operations Karl Mueller (an organizational veteran who recently received a new job title more reflective of his duties, Stearns said) and manager of baseball contracts Matt Kleine.
Flanagan takes over a Brewers farm system that has received an infusion of talent over the past calendar year, with the team shifting away from the sort of "go for it" trades that cost prospects like Brett Lawrie and Lorenzo Cain earlier in the decade to a rebuilding period. Ten of MLBPipeline.com's top 30 Brewers prospects are new to the organization in the past calendar year, either by trade or the Draft, including No. 2 prospect Brett Phillips, who was one of four prospects acquired from the Astros in July.
"It's definitely a very exciting time," Flanagan said. "I go back to my days as assistant scouting director, where the big league club scuffled there in the early 2000s. Working on the scouting side, you could almost see it coming. You could see the talent assembling in the Minor Leagues.
"... This may be a parallel. We have a ways to go, certainly. We need to continue to add more players. But there is a good foundation in place now that can be built upon."
Flanagan earned a degree in business administration from the University of Wisconsin-Milwaukee and lives in New Berlin with wife Jennifer and their two children.