Mr Wilson, a director of the Auckland-based company since 2003, will take up the new role when Mr van der Heyden steps down at the annual meeting in December.
"John brings lengthy experience in the dairy industry," Mr van der Heyden said.
Mr Wilson is a previous chairman of Fonterra's shareholders' council and has interests in two dairy farms - one where he lives near Te Awamutu and a dairy farming business in Geraldine, South Canterbury.
Separately, Ian Brown has been elected new chairman of the shareholders' council, with Philip Palmer named as his deputy after a vote by councillors on Wednesday.
