Boylen went 39-84 over two seasons.
"After doing a comprehensive evaluation and giving the process the time it deserved, I ultimately decided that a fresh approach and evolution in leadership was necessary," Arturas Karnisovas, Chicago's executive vice president of basketball operations, said in a statement. "This was a very difficult decision, but it is time for our franchise to take that next step as we move in a new direction and era of Chicago Bulls basketball.
"Jim is a great human being that cares deeply about this organization and the game of basketball. I want to thank him for his professionalism and commitment to the franchise."
Denver Nuggets assistant Wes Unseld Jr., former Brooklyn Nets head coach Kenny Atkinson, Toronto Raptors assistant Adrian Griffin, and Milwaukee Bucks assistant Darvin Ham are expected to be considered as replacements, ESPN's Adrian Wojnarowski reports.
The Bulls were not invited to the season's restart in Orlando this summer after mustering a 22-43 record under Boylen before the stoppage. The 55-year-old also appeared to clash with his players, including Zach LaVine.
Multiple key players are said to have "ripped" Boylen during discussions with Karnisovas and new general manager Marc Eversley in May.
Boylen first joined the Bulls as an associate head coach on Fred Hoiberg's coaching staff in 2015. He was promoted in December 2018 after the team fired Hoiberg following a 5-19 start to the campaign.