A baby has died from whooping cough in South Australia for the first time in almost a decade.

The five-week-old Adelaide boy died in intensive care in hospital this week.

No other details have been released about the tragedy.

Professor Paddy Phillips from SA Health said: "It's a tragedy and my sincere condolences go out to the family. We want to make sure that these things don't happen."

He said immunisation remains the best protection against whooping cough, but babies younger than six months cannot be given all the required vaccinations.

There have been nearly 4,000 cases of whooping cough in SA this year, a rise of about one-third over last year.

There have been six deaths from the infection in SA since it was declared a notifiable disease in 1990.