Under Ivanisevic's guidance, Cilic claimed the 2014 US Open for his one and only grand-slam success.
Cilic recently reached the Wimbledon quarter-finals, but announced the end of his partnership with Ivanisevic – a former champion at the All England Club.
"Unfortunately, I am no longer working with my coach Goran Ivanisevic," the 27-year-old wrote on his website.
"We have started to work together in September 2013 and we had a lot of success during that period, especially winning the US Open in 2014.
"It was huge privilege to work with Goran, I enjoyed our work all this time and Goran helped me to reach many goals.
"Unfortunately, the road we were sharing on this journey is separating and I wish only the best for Goran in the future."