The 42-year-old has previously worked as the Under-18s coach at Wigan Athletic, as well as having spells in the academies of Everton and Liverpool respectively.
"I'm thrilled to be able to bring John to Hibernian - he is a quality coach with an excellent pedigree," Stubbs told the club's official website.
"I've known him for a long time and I completely trust his judgement. He will be able to implement fresh ideas to improve our squad and his appointment is a real coup for Hibernian."
Hibs get their Scottish Championship campaign underway at home to Livingston on August 9.