The 80-year-old man was the second reported case of H7N9 infection in Hong Kong after one reported on December 2.
A government spokesman confirmed the death of the man, who had been suffering from other underlying medical conditions.
He had been taken to hospital after returning to Hong Kong from the neighbouring city of Shenzhen in mainland China, where he lives.
Hong Kong officials have stepped up border checks and traced hundreds who had been in contact with the two people infected.
The first case involved a 36-year-old Indonesian domestic helper who also had a history of travelling to Shenzhen.
Health officials had expected human cases of avian influenza in low winter temperatures, given the number of cases in mainland China.
In all, 138 human cases of H7N9 have been reported in mainland China since February with 45 deaths, according to the World Health Organisation.
Hong Kong is especially alert to the spread of viruses after an outbreak of Severe Acute Respiratory Syndrome swept through the city in 2003, killing 299 people and infecting around 1,800.
Journalists are reported to be among the men who were forcefully searched
Here's a guide for Class 10 and 12 students who are appearing for the exams in 2024