Yunus''s resignation came as he lost his final legal battle in the apex court to thwart a Bangladesh Bank decision removing him from the position on Mar 2.
Deputy Managing Director Nurjahan Begum will take over from Yunus until the board names a chief.
"I am today relinquishing the post of Managing Director of Grameen Bank on the basis that the Deputy Managing Director Mrs Nurjahan Begum would hold charge until a Managing Director is appointed in accordance with the procedures under section 14 of the Grameen Bank," Yunus said in a statement issued last night.
Authorities said he was over the legal retirement age, but supporters say his dismissal was politically motivated.
Bangladesh Bank, which is nominally independent from the government, fired Yunus as the central bank found that his 2000 appointment as the Grameen Bank's executive chief was faulty because the central bank''s mandatory approval was not obtained at that time.
His troubles stem from 2007 when he announced formation of a political party. The idea was visibly unwelcome by Prime Minister Sheikh Hasina and her arch-rival Khaleda Zia of Bangladesh Nationalist Party (BNP). He himself abandoned the idea of joining politics within months.
Yunus said he decided to resign "without prejudice" to the legal issues and to prevent "undue disruption of the activities of Grameen Bank and to ensure my colleagues and our 8 million members, and owners of the bank, are not subjected to any difficulty in discharging their responsibilities".
"I hope Grameen Bank will continue to operate maintaining its independence and character under the Grameen Bank Ordinance and move towards even greater success," he said.
Yunus''s resignation came hours after finance minister AMA Muhith rejected possibilities of his appointment as ceremonial chairman of the Grameen Bank.
"It is not possible to make him the chairman [of Grameen Bank] because of differences of opinion among the employees of the Bank about the proposal," he said.
Yunus''s experiment of poor men''s banking earned Bangladesh the repute of being the home of microcredit. He had founded the bank in 1983.
He and his Grameen bank were jointly awarded the Nobel Peace Prize in 2006 for helping millions out of poverty with small loans. The Grameen Bank model was copied in a number of developing and developed countries.