Global Crossing vice chairman Thomas Casey has been picked to lead the company, which builds undersea and land-based fiber-optic telecommunications networks.
The Hamilton, Bermuda-based company said Hindery is resigning by mutual agreement.
Hindery, who is also chairman and chief executive of GlobalCenter, Global Crossing's Web hosting subsidiary, will continue in those roles until completion of the sale of GlobalCenter to Exodus Communications, which is expected early next year.
The GlobalCenter Web-hosting business offers storage and maintenance facilities for Web sites and other Internet services such as applications management. Global Crossing has been working to aggressively build its data and Internet operations.
Hindery's resignation comes as the company has seen its stock fall steadily in recent months from a 52-week high of more than $61 to about $23.
But Hindery will leave about a quarter of a billion dollars richer, according to a Bloomberg report.
Almost all the pay stems from a provision Hindery negotiated in his employment contract guaranteeing that in the event GlobalCenter would be sold, Hindery would receive 5.5 percent of any amount more than $2 billion, Bloomberg reports.
Hindery, a former AT&T executive, in March replaced Bob Annunziata, another former AT&T executive, as CEO of Global Crossing.
Casey, 48, is vice chairman of Global Crossing's board, a director, and a member of its Office of the Chairman. He previously served as co-head of the global telecommunications investment banking group at Merrill Lynch and co-head of the worldwide telecommunications legal practice at Skadden Arps Slate Meagher & Flom, according to Reuters.
The chief executive shuffle follows several changes in the leadership of the company last spring. In May, the company replaced co-founder David Lee with former IBM executive Gary Cohen as chief operating officer and announced that Joseph Perrone, a senior partner at consulting firm Arthur Andersen, would serve as vice president of finance.
Executives were quick on Wednesday to point out that the chief executive move is the last change in the company's top management.
"We have brought in a very talented group of executives," Casey said during a teleconference. "Now there will be no changes in the short term or long term" in the leadership of the company.
Casey also said he has no immediate plans to leave the company. "I intend to be the CEO for the future. There is no interim attached here. My intention is to be here for the rest of my career."
Reuters and Bloomberg contributed to this report.