Kevin Curran has quit as general secretary of the GMB union three weeks after being suspended from its executive committee.
The union said an amicable agreement had been reached with Curran and the decision was in the "best interests" of the wider trade union movement.
He was suspended on full pay last month during an inquiry into alleged ballot rigging during the union's leadership election.
The union said in a statement: "He leaves the GMB with his reputation and integrity intact and the GMB wishes him well in whatever path he chooses to follow in future employment.
"Each party has agreed to keep the terms of the settlement confidential. Neither party will be making any further statement."