The man, whose identity was not revealed by the state directorate of health services, died at a government hospital last night.
He hailed from Sanguem village.
Dr Utkarsh Betkekar, state epidemiologist, confirmed that it was a swine flu infection case.
Of the 25 samples sent to national disease control centre in New Delhi by the state authorities this year, eight samples (including that of the man who died yesterday) tested positive for H1N1 virus.