The win comes after a pitch against Bartle Bogle Hegarty London and two unnamed European agencies.
The pitch was called in April as TNT considered developing a new marketing strategy and targeting a wider, particularly European, market.
TNT did not have a retained above-the-line agency, but in the past, J. Walter Thompson has handled the business internationally. In 1996, JWT developed the company's "We take it personally" strapline and also branded TNT with the orange colour it still uses today.
David Miller, the managing director of W&K Amsterdam, said: "We are looking forward to working with TNT - it is an exciting company with big plans."
TNT operates across most of the major countries in Europe, Asia and Australasia.
In addition to its express service, TNT operates two other divisions: mail and logistics.
At present it is preparing for the launch of TNT Mail in the UK and last week it appointed Simon Dolph as the head of marketing and communications for the new service.
TNT Mail's ambition is to become the main challenger to Royal Mail amid the deregulation of the sector. It has recently agreed a two-year deal with the milk delivery service Express Dairies to deliver its heavy packages, enabling it to extend its reach and services within the country. However, there are no plans to market this division.
TNT was not available for comment.