In a short statement, the ECB said Friday that Stark, 63, had decided to resign "for personal reasons" before the end of his term of office in May 2014.
ECB watchers, however, suggested Stark's departure could point to deeper differences among EU and eurozone policy makers over the way out of the current debt crisis.
Stark has been critical of the bank's controversial programme of buying bonds of eurozone countries who find themselves unable to affordably borrow on the markets.
In a commentary to be published Monday in the German daily Handelsblatt, Stark called for drastic reforms to strengthen economic governance of the eurozone.
"We find ourselves in a situation where risks to public budgets undermine financial stability," wrote Stark.Schaeuble said Friday the German government "regrets and acknowledges with respect" Stark's decision to step down, adding that Berlin would make "a good proposal" for his succession.