Carroll will remain in the top job until a successor is appointed to allow for a smooth transition.
The US-born geologist was appointed to the Anglo board in January 2007, succeeding Tony Trahar, and formally took over as CEO in March of that year.
She had previously spent 18 years at Alcan, where she was CEO of its Primary Metals Group.
Carroll said it had been an honour to lead Anglo.
“I am extremely proud of everything we have achieved during my period as chief executive and I will always retain enormous admiration and affection for this great company and its outstanding people,” she said.
“It is a very difficult decision to leave, but next year I will be entering my seventh year as chief executive and I feel that the time will be right to hand over to a successor who can build further on the strong foundations we have created.”
Carroll will also step down as chairman of Anglo American Platinum and De Beers.
Anglo chairman Sir John Parker will lead the search for Carroll’s successor and expressed his appreciation for her willingness to stay on until a replacement was found.
“Cynthia’s leadership has had a transformational impact on Anglo American,” he said.
“She developed a clear strategy, based on a highly attractive range of core commodities, and created a strong and unified culture and a streamlined organisation with a focus on operational performance.
“Her legacy will include, among many other things, a step change improvement in safety, sustainability and the quality of our dialogue with governments, communities and other stakeholders.
“Her values represent the very best of Anglo American.”
London-based Numis Securities rated the change as a negative for the company, despite it being touted in the press for some time.
"Given the challenges and pressures to the business it may not come as a surprise to some, but we believe overall she has done a good job of transforming the company since taking the helm in 2007," analysts said in a morning note.
"Only in the recent year or so have things started to falter, mainly around the platinum sector and the recent industry problems endemic in South Africa.
"In our view, she should leave with her head held high."