"I've been impressed with the club's ambition and the people driving the club forward," said McPherson. "It's an interesting project; the club has great support at matches so I'm looking forward to being a part of that - without doubt the club is unique."
McPherson will head an expanded coaching team at Waiheke, with current first team coach Nick Saunders remaining in the fold.
"They've created a winning culture, which we'll be working towards continuing. I'm looking forward to working with the current coaching staff and to seeing the players in pre-season."
Read more: Chris Wood scores in Burnley win
Waiheke United AFC Club President David Arnold says securing the services of McPherson was a coup for the club.
"We are on a journey and certainly we have enjoyed great success over the past six seasons," said Arnold. "We feel he is a great fit for the culture we have developed here at Waiheke."