Ann Marr, who is currently chief executive of the neighbouring hospitals trust at St Helens and Knowsley, will replace Ian Dalton from October 3.
Mr Dalton is leaving the post to take up a similar position with the University Hospitals of North Tees and Hartlepool.
Alan Massey, chairman of North Cheshire Hospitals, said: "I am delighted that someone of Ann's calibre and experience has agreed to lead the trust for a period of time."
Ms Marr is an experienced NHS chief executive who has achieved a three-star rating within her own trust and her support will enable the trust to continue the major improvements in patient care that Mr Dalton has led over the past two years.
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