Hayes, who spent eight years on the Melbourne board, is the fourth board member to step down following the sacking of former coach Mark Neeld.
Former president Don McLardy and Stuart Grimshaw were the first to depart, followed by former vice-president Guy Jalland, who resigned on Monday.
Board member John Trotter has been appointed to evaluate the boar's processes, structures, composition and skill, and he is expected to deliver his findings to the club's next board meeting in July.
“It is now time for the next wave of expertise to come in to take the club forward into its new direction," Hayes said ahead of the Demons' clash with the Western Bulldogs at the MCG.
"I am extremely confident we're in very good hands with Peter Jackson, the club's new and highly-credentialled CEO.
"We also have some truly outstanding people within our club, both on and off the field.
"Together, along with the welcome support of the AFL, I have no doubt that Melbourne will realise its rightful place at the top of the ladder."
Club president Peter Spargo said Hayes had given the club great service.
"Karen has been an outstanding contributor to the Melbourne Football Club for almost a decade and she should be commended for her leadership, governance, expertise, passion and ability to relate and engage with a wide range of people," he said.
"Karen was instrumental with Melbourne's Field of Women, the Women of Melbourne committee, our women's football program and the Dare to Dream programs and events."
Nathan Schmook is a reporter for AFL Media. Follow him on Twitter: @AFL_Nathan
