Sir Ben led the NFU through the foot and mouth epidemic in 2001 as well as the final part of the BSE crisis.
He said there were still “enormous challenges” ahead, but that it was time for him to stand aside and give someone else the opportunity to “stamp his or her mark on the future”.
Sir Ben became president in 1998, before that he was deputy president, vice president and livestock chairman.
Meanwhile, the NFU has backed plans for a merger between the National Association of Farmers’ Markets and the Farm Retail Association.
The move would make it Britain’s largest farm retailing representative body.
Discussions about a merger began in January, and members will vote on a shared business plan at an Extraordinary General Meeting on October 14.