A release from the Bucks stated Skiles and the team "mutually agreed to part ways."
"Scott and I met (Monday) after practice and after some honest discussion, we both came to the conclusion that it was best to part ways," Milwaukee General Manager John Hammond said.
"It is never an easy decision to make but in the end a decision we felt was best for both parties. I want to thank Scott for his hard work, dedication and the imprint he leaves on our team and our entire organization. We all wish him and his family well."
Milwaukee, which has lost its last four games, is 16-16 this season, three games behind the Central Division-leading Chicago Bulls.
Skiles, 48, was hired as the Bucks' coach in April 2008. In three full seasons plus 32 games in 2012-13, Milwaukee was 162-182 under Skiles. The Bucks made the playoffs once with Skiles as coach, losing a first-round series against Atlanta in seven games in 2010.
Skiles previously coached the Bulls and the Phoenix Suns. In 13 seasons as an NBA head coach, Skiles built a 443-433 record.
Boylan, 57, had been the lead assistant for the Bucks for four seasons. He's worked with several NBA teams but his only head coaching experience was in 2007-08 as interim coach at Chicago. The team posted a 24-32 record.