Milwaukee Brewers (2015–present)
After the 2015 season, the Milwaukee Brewers hired Murphy as bench coach for Craig Counsell's coaching staff; Murphy was Counsell's coach during his playing career at Notre Dame. On June 11, 2023, Murphy filled in as manager for Counsell, who missed the game due to his son's graduation. The Brewers lost the game 8-6.
After the 2023 season, Counsell accepted the managerial position for the Chicago Cubs. On November 16, the Brewers promoted Murphy to serve as their new manager.
Before the 2024 season, some analysts and reporters predicted the Brewers would finish low in the NL Central due to Counsell’s departure, the loss of several players including star pitcher Corbin Burnes, and Murphy’s limited experience as an MLB manager. Under Murphy, however, the Brewers exceeded expectations. On September 18, the Brewers became the first team to clinch a postseason spot and won the NL Central. They finished the regular season with a 93–69 record, tied for the fourth-best record in baseball, and played the New York Mets in a Wild Card Series. Milwaukee lost to the Mets in 3 games. For the unexpected success despite significant injury troubles and starting pitching woes, Murphy was awarded the NL Manager of the Year Award, the first Brewers manager to earn this distinction.
In 2025, Murphy led the Brewers to the best record in the league and in franchise history, going 97–65 and winning the NL Central. The Brewers faced the rival Cubs in the NL Division Series, ultimately winning the series 3–2. They would go on to be swept 4–0 by the eventual World Series champion Los Angeles Dodgers in the NL Championship Series. The Dodgers held the Brewers to only 14 hits (or a .118 batting average) over the 4 game sweep-which is the worst offensive performance by any team in a 7-game postseason series in MLB history.
On November 11, 2025, Murphy was awarded NL Manager of the year for a second consecutive season. Cleveland Guardians manager Stephen Vogt won AL manager of the year in 2024 and 2025, marking the first time both leagues had repeat winners of the award in the same season. Murphy and Vogt are also the first managers to win the award in their first two seasons managing a team.
On February 19, 2026, Murphy and the Brewers agreed to a new three-year contract with a club option for the 2029 season, which included $8.95 million in new money.