Northland District Health Board (NDHB) medical officer of health Jonathan Jarman said the board had been notified that a 14-month-old from the Bay of Islands area had died from the Meningococcal B strain.
Meningococcal disease was an unpredictable disease, Dr Jarman said, and an investigation into the death would be led by the Te Tai Tokerau Primary Health Organisation, which would look at the GP's management of the case.
The child had become unwell on October 14 and was taken to an after-hours GP service, operated by the Te Tai Tokerau PHO at Bay of Islands Hospital in Kawakawa.
"Tragically, the child died at home in the early hours of Monday, October 15," he said.
"This is the first death and the third case of meningococcal disease in Northland so far this year.
"Earlier in October there was a 13-month-old boy, and in March there was an 8-month-old girl. Neither case was fatal."
Dr Jarman said he had met with the child's family, and described it as one of the saddest cases he had seen.
"Initially, it can present like the flu or a tummy bug, but the difference is meningococcal disease can get worse very quickly.
"Some people do not even get sick when they catch the bug. However, a small number rapidly develop invasive meningococcal disease," Dr Jarman said. "This case was an example of how quickly meningococcal disease can progress, and I understand the sorrow and anger the family are dealing with at this time."
He said it was important that parents seek medical advice if their child became unwell.
"If your child is sick, take them to the doctor. And if they don't get better, or if you are worried, go back to the doctor."
This year had seen the fewest reported meningococcal cases in Northland since 1991, he said. From 1992 to the mid 2000s, there was an epidemic of serogroup B disease in New Zealand.
In 1997, Northland experienced a spike in cases, with a total of 43, including two deaths. The meningococcal serogroup B vaccination campaign finished in 2008.
Last year, three people died from meningococcal disease in Northland, including Whangarei 18-year-old Ben Brown, who died after being twice sent home by medics at Whangarei Hospital.
For more information about meningococcal disease, see your doctor, practice nurse, medical centre or contact your local public health service.
For free advice after hours (24-hour service) phone Healthline 0800 611116. An investigation has been launched after a Northland toddler died from meningococcal disease hours after being seen by a GP.