"This confirmed case puts the number now at 107 infected, including 86 dead," Ningrum, a doctor from Indonesia's bird flu information centre, told AFP.
The victim, identified only by the initials "AR", died on Friday at a hospital in West Jakarta, said Ningrum.
He had tested positive for the H5N1 virus in two separate tests, the requirement to be reported as a confirmed case in Indonesia.
The man first suffered flu-like symptoms 10 days earlier but was only admitted to hospital three days before he died, Ningrum said.
It was not known whether he had come into contact with infected poultry, the usual method of transmission, she added.
"On the risk factors, we have nothing yet but a team (from the health ministry) is currently at his home," she said.
H5N1 is endemic in birds across nearly all of archipelagic Indonesia.
Scientists fear that the virus will eventually mutate into a form easily transmissible between humans, triggering a disastrous global pandemic.