Thomson, who has 17 years’ experience at senior levels in the Scottish government under his belt, will take on the role in December this year.
He was head of Food, Drink and Rural Communities for five years and is currently deputy director for primary care.
Thomson said: "Scotland's food and drink industry is world class. It will truly be an honour to represent such a vibrant sector and one with such potential to contribute even more to our national economy and community. I am looking forward to the challenges of ensuring Scotland's food and drink industry's bright future.”
FDF director general Ian Wright said: “David's breadth of experience of food and drink policy makes him the ideal candidate to take up the mantle and represent the sector in Scotland. With David's help we will continue to champion UK food and drink as a world leading industrial sector and outstanding national asset.”
Nearly one fifth (19%) of Scotland’s manufacturing workforce is employed in the food and drink industry, while Scotland Food and Drink has set a target of £16.5bn (€23.6bn) in turnover for the country’s food and drink sector by 2017.