Stanton replaces Arthur Papas - who resigned last week - having spent eight years at Sydney FC including five seasons as Steve Corica's assistant, winning two championships and a premiership.
He faces the challenge of taking the Jets back to the finals for the first time since they made the 2017-18 decider under Ernie Merrick.
"Rob comes to us from a winning club and knows how to drive success," Jets executive chairman Shane Mattiske said in a statement.
"He is highly rated by the leading figures in the game and now is the chance for him to step into the lead role and build on the foundation that has been established here over the last two years.
"Rob is a coach who has a great technical expertise and knows how hard you need to work to gain success, but importantly he is also someone who knows how to bring a team together to perform.
"Rob is driven to succeed and can see the potential that exists in the current team and the club as a whole.
"He is also a strong believer in the importance of developing youth and is committed to bringing through talent that is emerging in this region."
Stanton's first game at the helm will be the July 17 Australia Cup play-off against Melbourne Victory in Darwin.
"I'm excited to get started at the Jets," he said.
"There's a great culture here and we want to create a strong football environment for our players and staff.
"There's a lot of good people in Newcastle and we want to take the team to the next level and help our players further develop and challenge themselves.
"We want to get good people from the local community involved.
"I want this team to be a side that the Newcastle region is proud of as we work tirelessly to try and achieve our goals."
Stanton had an impressive career as a player, predominantly for Sydney United and Wollongong Wolves, including winning the NSL championship with the latter in 1999–2000 and 2000–01.
His Jets predecessor Papas, who had been frustrated at Newcastle's ownership limbo, quit with a year left on his contract. He has since been appointed technical director of Thai club Buriram United.
The Jets have been under the control of a consortium comprising several fellow A-League clubs after previous owner Martin Lee was stripped of the licence in January 2021 for failing to inject any money into the club or pay off debts.
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