The infant — understood to be under six-months-old — was brought to the hospital on June 13.
Anyone who came into contact with child were contacted and provided clearance antibiotics to prevent further transmission.
The tragic case is the fifth meningococcal infection in the Northern Territory this year, with the other four cases all being from the W strain.
According to the Centre for Disease Control, none of the cases were linked.
Meningococcal disease usually takes the form of a blood infection or an infection of the membranes covering the brain and spinal cord.
These infections can develop quickly and can cause serious illness or death. Early diagnosis and treatment with antibiotics are vital.
The meningococcal ACWY vaccine is available free for people aged 1-19, while the B vaccine must be purchased.
Darwin woman Mary-Ellen Hurley, 34, died from meningococcal disease on New Year’s Eve after presenting at the Palmerston Hospital emergency department.
The Centre for Disease Control urges people to be vaccinated against meningococcal disease.