AIS won the business following a pitch late last year.
Its brief is to increase sales for the summer holiday period through the Thomson.co.uk portal and travel agents.
The digital appointment is the latest in a series of changes made by Thomson to its agency relationships.
It appointed Krow to handle its creative account last November, replacing DDB London. Thomson also selected the direct marketing agency WDMP to oversee its DM in an attempt to increase booking levels. Its work has included targeting existing customers with mailings.
Nathan Timmins, the head of online marketing at Thomson, appointed AIS as the online company ups its online presence as it takes on digital specialists such as Expedia and lastminute.com.
Last October, Thomson hired the search specialist Spannerworks to work on its search marketing. Thomson also signed up as the sponsor of the Yahoo! Answers travel section.
Timmins was unavailable for comment.