The decision follows a three-way pitch against Carat and OMD. Ebookers said the account is "significantly more" than the £500,000 it was previously reported to be worth.
MediaCom will be charged with the overall media strategy for the online travel company, which aims to increase its share of the competitive online travel market in 2008.
Ebookers plans to launch a new website and rebrand in April in a bid to build its consumer brand against rival travel brands such as Expedia and lastminute.com.
It currently works with Conrad Advertising to buy and plan its classified advertising, but it is uncertain whether this relationship will continue.
Ebookers appointed Conrad last year, along with the direct marketing specialist Hall Moore CHI, which was hired to handle its direct- response advertising.
Ebookers was acquired by Travelport in February 2005. Travelport operates more than 20 travel brands, including the online travel agency Orbitz and the global travel content wholesaler GTA.