Goodstuff will work on a £1 million communications brief to support the network of visitor attractions. Activity begins with two TV campaigns to support the Edinburgh and York sites over Easter.
Other projects Goodstuff is likely to develop include film associations, street theatre and brand partnerships.
Scott Williamson, the head of marketing at Merlin, said: "We were looking for an agency to challenge the way we approached our communication and Goodstuff brought fresh creative perspective."
Goodstuff's appointment follows The Leith Agency's selection to handle creative duties and M2M's to handle media buying. Thomas Media Consultants will handle outdoor media buying and OMD Netherlands, media buying, for the Amsterdam Dungeon.
Separately, Goodstuff has hired Jonathan Fraser, formerly a strategist at Rocket, to work on its Chariot Lottery and Ann Summers business.