Boylen posted a 69-60 record with one NCAA Tournament appearance, but a downturn to seasons of 14-17 and 13-18 in his last two years cost him his job.
Boylen joined the Bulls in 2015 when Hoiberg was hired.
Between his stints as an National Basketball Association assistant coach that have totaled 20 seasons, Boylen worked as a Michigan State assistant and was hired by then-Utah athletic director Chris Hill as the replacement for Ray Giacoletti in 2007. He did spend four years as the head coach at the University of Utah.
The Associate Head Coach Jim Boylen has been promoted to head coach. During his stint in Chicago, the Nebraska native coached the team to an overall record of 115-155. His tenure with the Bulls began on June 2, 2015.
Hoiberg was in a tough position this season with four of the team's top players getting injured, a painful run that started early in training camp.
Last season, the first of a full rebuild following the trade of Butler to the Timberwolves, the Bulls finished 27-55 and drew widespread praise throughout the league for their competitiveness and player development.
He replaced Tom Thibodeau, who was sacked after five seasons.
The circumstances were different, but the results were disappointing. Denzel Valentine (ankle), Kris Dunn (knee) and Bobby Portis (knee) have missed significant time, and forward Lauri Markkanen didn't make his season debut until this past weekend because of an elbow injury.
The Bulls have been in the midst of a major rebuild since previous year, after jettisoning veterans like Dwyane Wade and Rajon Rondo, and trading Jimmy Butler to the Minnesota Timberwolves for for guard Zach LaVine, point guard Kris Dunn and the rights to the No. 7 pick in the 2017 draft.
The Bulls reportedly do not intend to hire an assistant to replace Boylen for now.