Emergency services were called to Vaucluse in the city's east to reports of a shark attack about 4.20pm on Sunday.
The boy was pulled from the water off Shark Beach by NSW Police and Marine Area Command officers "within minutes" of the call being made to triple zero, police said.
Water Police officers attached two medical tourniquets before administering first aid on board a police vessel.
The teenager was taken by boat to nearby Rose Bay Wharf, where he was treated by NSW Ambulance Paramedics for serious leg injuries.
A short time later, he was transported by road to Sydney Children's Hospital in a critical condition, a NSW Ambulance spokeswoman said.
"The injuries are consistent with what is believed to have been a large shark," police said in a statement.
The incident happened near Nielsen Park and Shark Beach, a popular swimming spot for families that has a netted area in Sydney Harbour.
Footage from the scene showed the boy being treated by paramedics in a police rescue tent with multiple ambulances nearby.
The beach has been closed and swimmers have been advised not to go in the water.
Agriculture Minister Tara Moriarty said the Department of Primary Industries and Regional Development was working to identify the species of shark involved in the attack.
"This is a tragic shark attack on a young boy having a swim on a Sunday afternoon in a harbour beach in Sydney's east," Ms Moriarty said.
"Our thoughts are with the young boy and his family.
"I understand there were also a lot of young people on the beach at the time of the attack. Our thoughts are also with them."
Multiple swimmers have been attacked by sharks in Sydney Harbour in recent years, including a young woman who was bitten on the leg at Elizabeth Bay in early 2024.
A 57-year-old surfer died when he was attacked by a shark while swimming at Long Reef Beach on Sydney's northern beaches in September.
A Swiss tourist was killed by a shark two months ago while swimming at a remote beach on the NSW mid-north coast.
The woman, aged in her 20s, was attacked at Kylies Beach in the Crowdy Bay National Park in November.
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