He successor will be current vice-president Mark LoGiudice, who will be officially appointed at a Carlton board meeting on June 23.
LoGiudice, who has been a director at the club for four years, spoke briefly at the club's pre-game function at Etihad Stadium on Saturday.
He told guests he was humbled to be appointed as the Blues' next president.
"My approach as president will be to provide the stability and governance to unite all aspects of our club that will help us and enable us to flourish," LoGiudice said.
"Carlton is a great club. Despite what all the reports have been over the past few weeks, Carlton is a great club and the vast majority of us have grown up in an era of great success and that is what we all want to return to."
During his four years as director LoGiudice has chaired Carlton's club member venues committee and sits on its finance, audit and risk committee.
However he was not outlining any grand plans at the time of the announcement.
"At the appropriate time in the very near future I will be talking to you with more detail about how we move forward. It is with a genuine passion for the Carlton Football Club that I look forward to leading us through the next chapter of our rich history," LoGiudice said.
LoGiudice is the Managing Director of Crawfords Group, a Carlton member and supporter for more than 19 years of the club coterie group, Carltonians.
He is also a director of Premier Fruits Group, a national farming, marketing and logistics company.
Kernahan, a premiership captain at the Blues and member of the AFL Hall of Fame, will stay on the club's board until the end of the season to ensure a smooth transition. He has been Carlton president since 2008.
