Rowntree stands down as Munster coach after two years in charge
The former England prop's exit, revealed in a joint statement by Munster and the Irish Rugby Football Union, comes after two years in charge.
Rowntree, 53, led Munster to the United Rugby Championship title in 2023 - their first trophy in 12 years - having been promoted to head coach following three years in charge of the team's forwards.
But this season Munster have won just twice in six league games and currently lie 12th in the 16-team competition.
Munster's head of rugby operations Ian Costello takes over as interim head coach with immediate effect.
"We would like to thank Graham for his passion and dedication to Munster Rugby over the past five years, and I would like to wish him and his family the very best for the future," Munster chief executive Ian Flanagan told the province's website.
Rowntree added: "I have thoroughly enjoyed my time here in Munster working with a very talented group of players and coaches.
"I would like to thank the wider Munster family for all the support they have shown me in my time here, but now is the right stage for my family and I to look forward to a new chapter."