The sites have used some of The Search Works' software since 2005 but the relationship has been extended to include campaign management. The agency will work with moneysupermarket.com's in-house search team on future campaigns.
Comparison sites have gained in popularity in recent years, pushing up the price of key words as a consequence, and forcing the sites to increase their spend on search.
The contracts are the first The Search Works has picked up since TradeDoubler bought parent company IMW Group for £56m last month. They add to The Search Works' current clients which include Asda, Comet and Lastminute.com.