Duffy was marketing services director for Barclays Bank. Among his first challenges will be a campaign scheduled for debut this autumn, featuring the high performance R8 sports car.
According to Audi, this campaign will be followed by: "Intense communications activity that will gain momentum over the next two years."
Duffy said: "It's enormously exciting to be joining such an iconic and dynamic brand at such a pivotal stage in its development.
"This is obviously an already very well respected prestige marque with a long-standing reputation for 'Vorsprung durch Technik', and I relish the challenge of further raising its stock and realising its incredible potential."
Audi has been looking for a head of UK marketing since November, following the departure of Brotherton, who left the firm to become head of loyalty at sister firm Volkswagen.
Brotherton, had been in post since September 2005, and was previously marketing director for VW Commercial Vehicles. He replaced Gary Savage, who became head of operations.
He was responsible for the recent £5m ad campaign for the Audi A6, highlighting the fact that Audi had filed more patents than NASA in the development of the car, to promote its emphasis on technological advancement.