Earlier this month the Department for Children, Schools and Families announced it was ending funding for NCERCC, instead awarding private provider Tribal with the contract to run a new programme of "Support and Challenge for Children's Homes".
But today it has been confirmed that Stanley will remain at NCB, which houses NCERCC.
NCB chief executive Sir Paul Ennals said: "We are delighted to say that Jonathan Stanley has agreed to stay with us, to help us explore what future opportunities exist. We will be convening a meeting of some selected key agencies within the sector in the coming weeks to gather ideas as to what is possible.
"It has been gratifying to see the support we have received since the news of our unsuccessful tender bid. We very much want to continue to improve the experience and outcomes for children in residential care, building on our experience and our unrivalled contacts, if we can identify the funding."