Law Ho-ming had had a fever and a persistent cough for about two weeks before being hospitalized on March 6. He was later discharged, but rushed to the emergency department at Tuen Mun Hospital on March 8. The boy lapsed into a coma and was subsequently diagnosed as suffering from swelling of the brain.
The first postmortem tests have so far proved negative for influenza, however.
Another two children had earlier died several hours after being admitted to hospital in Hong Kong after displaying similar symptoms.
The Hong Kong authorities have instructed a team of microbiologists to attempt to determine the reasons behind the deaths.
Another 38 children from Law's school have also been diagnosed with similar flu-like symptoms. The school has now been closed a week ahead of the spring holidays.
The local Center for Health Protection said the amount of flu cases had not so far exceeded the usual seasonal figures. However, medics have recommended that school authorities cancel classes so as not to endanger children.
National media has quoted some doctors as saying the disease responsible for the deaths of the three children could be a strain of bird flu, which has so far killed 235 people out of 371 confirmed cases worldwide, according to the World Health Organization.
Six people out of a total of 18 residents infected with bird flu died in Hong Kong in 1997 when the first outbreak was reported in the former British colony.
Although no cases of human-to-human transmission of the deadly H5N1 strain of bird flu have been reported, scientists fear the virus could mutate into a strain that could pass easily between people, causing a global pandemic.
Between 50 and 100 million people died from so-called Spanish flu from 1918 to 1920. This is higher than the total amount of deaths in World War I. Recent evidence suggests the disease may have jumped from birds to humans.