Miller signed a two-year contract with the A-League club after recently leaving his role as assistant at English Championship club Fulham, where he worked for nine years.
Joining Miller as senior assistant coach at Jets is Jean-Paul de Marigny, who under Kevin Muscat with Melbourne Victory last season.
"Scott is an incredibly driven young Australian coach, who set off for England on a one-way ticket almost a decade ago and spent seven years in the English Premier League working with world-class players and managers," A-League chief Damien de Bohun said.
"He has shown the FFA Technical Staff that he has the right qualities, philosophies, qualifications and experience to take the step up to a Head Coach role and I'm delighted he's been secured for Newcastle Jets.
"Jean-Paul brings vast knowledge of Australian football and the Hyundai A-League, and like Scott has excellent qualifications and experience. Together, they make a compelling combination for the Jets."
At 33, Miller (not to be mistaken for the former Perth Glory player of the same name) will become the youngest coach in A-League history.
He was a part of the Socceroos' backroom staff in 2013 under Ange Postecoglou, who headed the panel in charge of finding a replacement for Phil Stubbins after he was axed when FFA took over from Nathan Tinkler last month.
Miller said he is thrilled to take charge of the Newcastle Jets at such an exciting time for the club.
"It's the right time and the right place for me," said Miller. "I jumped at this wonderful opportunity to take the next step in my coaching career as Head Coach at a club that's making a new beginning.
"I've heard a lot about the long and proud history of this football region and its passionate fans. Football clubs exist to bring joy to the people and that's a driving force in my thinking."
Miller and De Marigny will formally commence duties when the A-League squad begins pre-season training on Monday 6 July.
The licence for the A-League club in Newcastle is being operated by FFA.
