The move consolidates the publisher's offline spend with online, which covers both display and search activity.
Carat wins the £3.4 million offline business from MediaCom, while Carat's sister agency Diffiniti was the online incumbent.
The Auto Trader team from Diffiniti will now transfer to Carat to create a team working across all media.
Auto Trader's new agency arrangements follow a pitch process that also had MediaCom and ZenithOptimedia on the final shortlist.
Hurrell Moseley Dawson & Grimmer, which advised on the media pitch, has grown its relationship with the publisher. The agency, which last year launched the "Auto Trader land" campaign, is now lead communications strategy agency on the business.
Matt Thompson, the marketing director for Trader Media Group, said: "The pitch gave us the ideal opportunity to consolidate our agency portfolio and, by doing so, to create a more cohesive and streamlined approach for our overall media campaign."