At the same time, Nigel Connor, who joined the company in June 2009 as head of licensing, has been appointed company secretary with immediate effect.
Whitley replaces Kirk Davis, who will join Greene King from the start of next year as its new chief financial officer.
Whitley joined JDW as a shift manager in one of its pubs in September 1999 after reading mathematics at Durham University. He then moved into a number of internal audit and finance roles at head office. He qualified as a chartered management accountant in 2012.
Connor previously worked for McLellans Solicitors and qualified as a solicitor in 1997.
Chairman Tim Martin said: "The board is pleased to announce Ben and Nigel's appointment. Ben especially is an example to the rest of the company of the progress they can make."
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