Speaking to the club's official website, Stubbs said: "To be given this opportunity with Hibernian is a great privilege and a real honour. It is a massive club with huge potential.
"I'm excited about the future here at Hibernian and what we can all achieve together at the club - this is the start of the journey. The Scottish Championship will be a tough division, but I'm confident that if we approach the challenge with enthusiasm, optimism and belief then we can achieve success."
Stubbs had most recently been coaching the Under-21 side at Everton.