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Mr Wilson, who has been on the board since 2003, will take up the role when Sir Henry stands down at the annual meeting in December.
Sir Henry has been on the board since its formation 11 years ago, serving as chairman since 2002.
He announced at last year's annual meeting his intention to stand down at the next annual meeting.
A previous chairman of the Fonterra Shareholders Council, Mr Wilson farms near Te Awamutu and also manages a dairy farming business in South Canterbury.
Fonterra's board had been working through a process over the past two years to appoint a chairman-elect, Sir Henry said.
The two men would work together over the next few months to assist with a "smooth transition", Sir Henry said.
Federated Farmers hoped Mr Wilson would put in place a "clear succession pathway" by creating a deputy chairman.
A lack of board succession was a "strategic weakness" given Fonterra was a team made up of farmers, staff, customers and suppliers, dairy chairman Willy Leferink said.