The diagnosis was confirmed on Monday after the toddler's death last week, the fourth case of the disease in the Hunter and New England regions so far this year.
"This is a tragic event and our sympathies are with the child's family at this very difficult time," public health physician Dr David Durrheim said in a statement.
The child's family have been medicated to prevent further spread of the illness.
Dr Durrheim said the disease could occur year-round, but they typically saw cases peak in spring, after the winter flu season.
"Most cases occur in infants, young children, teenagers and young adults, although people of any age can be affected," he said.
Meningococcal does not spread easily and usually begins with a sudden fever - often with headache, nausea and drowsiness.
Neck stiffness, a dislike of bright lights and a rash of reddish-purple spots or bruises can develop rapidly and babies with the infection may be irritable, not feed properly and have an abnormal cry.
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