Clarke, who left Kraft earlier this year, had been in his post for two years, having previously run the company's operation in Australia and New Zealand. Prior to this, he was a category director with responsibility for marketing across Kraft's coffee and chocolate portfolio.
A spokeswoman from Burton's confirmed that the company's chief executive, Paul Kitchener, is to step down due to ill-health. However, she refused on comment on the identity of his successor.
During his tenure at Kraft in the UK, Clarke oversaw the repositioning of the Dairylea brand as a healthier product, and the decision to drop comedian Dawn French from ads for Terry's Chocolate Orange.
He also played a significant role in driving the company's ethical policies including its sustainable business strategy.Two years ago, Burton's Foods was bought by a venture capitalist and, since then, it has targeted the premium snacking categories sector with the roll-out of products such as Geo bars.
It is now the UK's second-biggest biscuit maker, after United Biscuits. It owns the Jammie Dodgers, Maryland and Viscount brands, and makes Cadbury biscuits and fingers under licence. Burton's recently appointed ad agency Fallon to the Jammie Dodgers account, while Adam & Eve handles Cadbury biscuits.
News of Clarke's move came as Kraft's £10.2bn takeover bid for Cadbury was rejected.