The Bulls went 24-32 after he replaced Scott Skiles Dec. 27.
"Letting a coach go is never easy," said Executive Vice President of Basketball Operations John Paxson in a statement. "Jim was put in a difficult position on Dec. 27, without the luxury of having a training camp and with some of the issues that arose during his time as head coach."
Chicago finished with a 33-49 mark and failed to make the playoffs.
The team qualified for the post-season in both 2006 and 2007 under Skiles.
Boylan, 52, was in his fourth season with the Bulls.
He was an assistant coach when he joined the team in 2004.
In 14 years as an NBA assistant, he also has worked for Mike Fratello in Cleveland, Brian Hill in Vancouver and Terry Stotts in Atlanta.