The Guardian reported that she quit after a 'difficult' meeting with health secretary Andy Burnham when it emerged in-vestigators were being sent to an Essex hospital because dozens of patients are thought to have died due to inadequate care.
A month earlier, the CQC had rated the quality of care at the hospital as good, leading to a row about the CQC's credibility.
Barbara Young said: 'Having overseen the major task of creating a single regulator for health and social care and pointed it in the right direction, I have decided that it will be for others to take it forward.
I wish all success to the commission and its staff and to Dame Jo Williams who has agreed to act as chairman until a successor is appointed. Jo will start to take up the reins in January.'
Shadow Conservative health secretary Andrew Lansley said: 'I believe Barbara Young wanted to end the flawed Healthcheck assessment system and to have better enforcement powers alongside the registration system from April. Her decision to leave before April demonstrates the breakdown between Labour ministers and their flagship regulator.'
Steve Barnett, NHS Confederation chief executive, said: 'In a complex healthcare system, the focus must be on getting clinical governance right at a local level. A regulator can only identify problems after they have happened.'