Stanton replaces Arthur Papas, who resigned last week, having spent eight years at Sydney FC, including five seasons as Steve Corica's assistant.
He started as the club's National Youth League (Y-League) coach in 2015 and won the title in 2016, while he also worked with Sydney's NPL team.
- Stream on ESPN+: LaLiga, Bundesliga, more (U.S.)
The Jets confirmed to AAP that Stanton, who announced his departure from Sydney FC on Monday, would be taking on the role.
"I've had a phenomenal eight years at Sydney FC and some fantastic opportunities to advance my career," Stanton said in a statement. "I feel this is the right time and right opportunity for me to move on and I'm looking forward to a new challenge."
Stanton 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.
Corica hailed Stanton's influence at the Sky Blues, which included helping the club to back-to-back ALM championships and the double in 2019 and 2020.
"Rob has been an excellent assistant and provided great support for the past five seasons," Corica said. "He is a dedicated football man with a very good tactical brain, and he deserves an opportunity to step up."
Stanton had an impressive career as a player, predominantly for Sydney United and Wollongong Wolves, including winning the National Soccer League 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.