Mark Goldring announced on Wednesday he would stand down from Oxfam GB at the end of the year in order to allow fresh leadership to navigate past recent criticism.
He rejoined Oxfam in 2013, about three years after the scandal, and the charity denied his exit is related to his handling of the fallout.
Mr Goldring said: “Following the very public exposure of Oxfam’s past failings, we have redoubled our efforts to ensure that Oxfam is a safe and respectful place for all who have contact with us. We are now laying strong foundations for recovery.
“I think that this journey will best be led by someone bringing fresh vision and energy and making a long-term commitment to see it through.”
Oxfam chairwoman Caroline Thomson said it was with “great sadness” she accepted the resignation of the man who battled the “test of a lifetime” at the charity.
Asked if the resignation is related to how he dealt with the crisis, an Oxfam spokeswoman said: “No, it’s absolutely not to do with his handling at all.”
Oxfam was plunged into crisis in February when it emerged some of its workers engaged in “sex parties” with prostitutes in the aftermath of 2010’s earthquake in the Caribbean country.
Mr Goldring apologised for the actions of charity staff when he appeared before MPs and also for his own comment to the Guardian that the charity was being attacked as if it had “murdered babies in their cots”.
Intense criticism over reports of sexual misconduct quickly led to the resignation of Oxfam’s then deputy chief executive, Penny Lawrence.
At that point, Mr Goldring said he would not step down unless the charity’s board lost faith in his leadership.
Mr Goldring, who first worked for Oxfam as Bangladesh country director in the 1990s, will continue to lead the charity until a successor is found.