The appointment follows the news earlier this week that Mark Hunter, Molson Coors UK & Ireland chief executive, was stepping down from the position at the organisation representing the pub and brewing sector after taking on a new role for Molson Coors.
A handover between Hunter and Neame is expected to take place before the end of June.
It is not the first role at the BBPA for Neame who has been a leading figure in the association for many years. He is currently a BBPA vice-chairman and executive board member and he moves from his current role as chairman of the BBPA’s Future Beer Group, where he has led campaigns against beer tax rises.
Neame joined Shepherd Neame in 1991 as company secretary until 1999 when he was appointed managing director. He became chief executive in 2003. He is also a non-executive director of the St Austell brewery Company.
Speaking about his new role Neame said: “In Britain we should all cherish and celebrate the role of beer and pubs. They are vital to the country’s economic, social and cultural life and with the right support should be a driver of growth, investment and job creation. I am passionate about the industry and honoured to step into the role at this time."
As well as operating the Spitfire and Bishop's Finger brands, Shepherd Neame owns and operates around 360 pubs across south east England.
Neame replaces Hunter whose appointment as chief executive of the central and eastern European brewer StarBev was announced earlier this week by Molson Coors, which recently acquired StarBev.
Hunter had only been in post as chair of the BBPA since December when he took over from Marston's chief executive Ralph Findlay.
Brigid Simmonds, chief executive of the BBPA, said: "I am delighted to welcome Jonathan as our new chairman, who brings huge experience of brewing and pubs. He is already a great champion of British beer, and also of the need for the industry to work closely together to ensure our voice carries weight with Government."
Earlier this week the BBPA announced J D Wetherspoon had joined the organisation which says its members account for around half of the pubs in Britain. Stefan Orlowski, Heineken UK managing director will now become BBPA vice chairman and Paul Wells, Charles Wells, chief executive becomes a BBPA director.