Case stepped down as AOL chairman in 2003 but remained on the media company's board. His departure comes as the media giant holds talks about the possibility of selling off a stake in AOL.
A number of high-profile technology companies including Google, Yahoo!, Microsoft and Comcast have shown an interest in taking a stake, but as yet no deals have been signed.
The interest comes despite AOL losing millions of dial-up internet subscribers every year as broadband takes off.
Case has been embroiled in scandal since the merger. In 2003, Dick Parsons, chairman and chief executive of Time Warner, and Case were subpoenaed by US financial regulator the Securities & Exchange Commission as part of its investigation into the company's advertising deal with Bertelsmann.
Questions about AOL's accounting resulted in shareholder lawsuits and investigations from regulators, all of which have been settled.
Case said he was leaving to spend more time at his new company Revolution, which provides healthcare and wellness programming and services.
"I strongly believe that AOL -- once the leading internet company in the world -- can return to its past greatness. Over the past few months I have been pleased to see a renewed focus on AOL at Time Warner and the emergence of so many strategic alternatives," Case said.
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