Boreyko is leaving in order to "continue the development of his musical career," according to a statement.
The WSO is assembling a search committee to seek a new music director with Boreyko's assistance. Some candidates will serve as guest conductors during the 2005-06 season.
Boreyko is also chief conductor of the Hamburg Symphony and principal guest conductor of the Stuttgart Radio Symphony. Before coming to the Winnipeg, he was chief conductor of Germany's Jena Philharmonic, and he remains honorary conductor of that orchestra.
"Maestro Boreyko has been a strong artistic leader," board president Carol Bellringer said. "We know he will be a lifelong friend of the WSO."
The WSO struggled financially during Boreyko's tenure, nearly shutting down in early 2003, but is well-regarded artistically.