Cr Wilson was elected by fellow councillors at the November 4 special council meeting.
Shire of Mundaring councillor Doug Jeans was chosen as the deputy chairman.
The council covers the Town, the Shire and Cities of Bayswater, Belmont, Kalamunda and Swan.
Cr Wilson said he was honoured to have received the trust and support of his fellow councillors.
“This is an exciting time for our regional council as we begin the process of implementing our newly endorsed FOGO (Food Organics Garden Organics) Recovery Strategy,” he said.
“I look forward to working with my fellow EMRC councillors and our dedicated team of hard-working staff over the next two years to ensure that we deliver quality services for the benefit of our six member councils and the residents of the eastern metropolitan region.”
Chief executive Marcus Geisler said the council was developing and implementing new strategies for waste management, FOGO and the WA Container Deposit Scheme.