McClarkin will start the role in early November, succeeding current chief executive Brigid Simmonds, who is stepping down to become chair of the new Betting and Gaming Council.
The new chief executive is currently working as a global consultant following a 10-year term as a member of the European Parliament (MEP).
Her past experience also includes chair of the Commonwealth Forum, director of global policy for the Sports Integrity Global Alliance and she is a special advisory board member at the Commonwealth Enterprise and Investment Council.
She has regularly worked with the BBPA, Brewers of Europe and Spirits of Europe, and was vice president of the European Beer Club during her time as an MEP.
BBPA chairman Simon Emeny said: “McClarkin has a genuine passion for beer and pubs, combined with the technical skills needed to champion this fantastic industry. She has drive and enthusiasm and I’m excited about the energy she brings to the role.
“Simmonds leaves an incredible legacy and a decade of excellent results. I’m really looking forward to seeing how McClarkin builds on this great work and utilises her past experiences and connections to further the success of British pubs and beer.”
Discussing her new role, McClarkin lauded the pub and beer industry and outlined her future plans for the BBPA.
She added: “The great British pub is an institution – it provides a home for the amazing beers we brew in the UK as well as a hub for local produce and local people.
“The industry is a showcase for innovation and how business can contribute to society and I’m looking forward to telling that story in my new role.
“I’m excited to be leading the BBPA as it continues to make sure this great community asset is protected, that British beer continues to be revered on the national and international stage and our industry is recognised for the amazing contribution it makes to the economy and the social fabric of Britain.”
The Campaign for Real Ale (CAMRA) boss Nik Antona welcomed McClarkin to her new role and looked forward to working with her in the future.
He said: “We’re delighted to hear Emma McClarkin has been named chief executive of the BBPA. She has supported CAMRA's events in the European Parliament for a number of years whilst acting as an MEP. We hope to continue that relationship as she takes on her new role at the head of the BBPA, working together on issues facing Britain’s beer drinkers and pubgoers.”