Bishop Donald Allister has been a member of the Council since 2006.
He is to succeed the Right Reverend Christopher Hill, Bishop of Guildford, who will be stepping down at the end of June after five years in the role.
Bishop Hill said the Council remained an "important instrument for the ecumenical thrust of the Church of England".
He welcomed the appointment of Bishop Allister as his successor.
"He has been a wonderful colleague on the CCU and in some detailed work we have done together," he said. "I shall leave the Chairmanship in the middle of next year with very positive feelings about its direction for the future with Bishop Donald.”
Speaking of his appointment, Bishop Allister said: “I feel deeply honoured to be asked by our Archbishops to follow Bishop Christopher as Chair of CCU. It has been a joy to serve on the Council since 2006 and, through that, to get to know and work with many of our ecumenical partners. Ecumenism properly understood - the sharing of faith, love, worship and witness rather than the bureaucracy - is vital. God is one and calls his people to be one and to love one another so that the world may believe.”