The organization released a statement Wednesday morning which said the team will relocate to Colorado Springs beginning in 2019.
The move comes as a result of the Brewers owners, Elmore Sports Group, wanting to realign a number of its clubs.
Once the Brewers move to Colorado Springs they will still be part of the Pioneer League.
As of right now it is unclear if Helena will get another team to replace the Brewers, or what will happen to Kindrick Legion Field.
Brewers General Manager Paul Fetz said the organization will try to make the most out of the situation in the next two years.
"We are going to have one heck of a memorable 2017, 2018 season," Fetz said. "It's going to be a lot of fun. I'm looking forward to Brewers baseball these two years and hopefully work with the staff closely to bring a championship here to Helena."
Fetz added the move to Colorado Springs "made sense" because the city is in a larger market.
The Brewers will still play in Helena the next two years.