Emergency CareFlight crews came to the rescue of a man and his dog in the Northern Territory after they became stranded in a boat in crocodile-infested waters.

A rescue helicopter was deployed to the South Alligator River in the Kakadu National Park earlier this month after the man in the boat activated his emergency beacon.

Upon arrival, both the man and his dog were safely winched from the vessel into the helicopter - neither had sustained any injuries.

"This was certainly one of the more memorable rescues for our team," Dean Blackney, Flight Nurse at CareFlight, said.

"We're trained for all kinds of scenarios, but it's not every day we winch up a dog!"

CareFlight said the successful rescue highlighted the importance of carrying an emergency beacon when travelling in remote areas.