The man in his 30s, who died at Royal Darwin Hospital, had no recent interstate or international travel, NT Health says.
"We send our condolences to this man's friends and family," a spokeswoman said on Friday.
The NT's centre for disease control is providing information and care to the man's close contacts.
The second case was a woman in her 30s from Alice Springs. The two cases are unlinked.
It comes after a 14-year-old boy in Adelaide was diagnosed with Meningococcal on Tuesday.
There have been nine cases of meningococcal disease in South Australia so far this year compared to six at the same time last year.
A Sydney man in his 40s died with the disease on August 4 after he attended the Splendour In The Grass music festival in Byron Bay.
There have been 15 cases of meningococcal disease reported in NSW this year.
Meningococcal disease is a rare but serious and sometimes fatal infection.
Authorities warn it can develop very quickly and kill within hours.
The bacterium is present in droplets discharged from the nose and throat when coughing or sneezing.
Anyone with a suspected meningococcal infection should consider their condition a medical emergency and see a doctor immediately.
The main symptoms of meningococcal disease are a red or purple rash, fever, headache, stiffness, light sensitivity, nausea, diarrhoea, drowsiness and confusion.
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