The number of infections in the territory has soared to nearly 500, said health authorities, adding more than 9,000 had been infected in the Chinese mainland -- doubling the average figure in recent years.
Local scientists say the outbreak may be linked to a deadly new strain of the disease which could make it more contagious than in the past.
It was discovered by researchers at the University of Hong Kong and appears to be resistant to antibiotics traditionally used to fight the illness.
"Test results showed that the five-year-old boy who died on Tuesday is confirmed to have suffered from scarlet fever," a spokeswoman from the Centre for Health Protection told AFP. The test results was released late on Wednesday.
The government said Tuesday the boy, who had chicken pox prior to his death, was "very likely" a victim of scarlet fever, after declaring an outbreak of the disease in the city of seven million.
The Centre for Health Protection spokeswoman said the boy's brothers, aged seven and 13, had also been tested for scarlet fever and results were still pending.
Classes have been suspended at the boy's kindergarten for a week, a first for Hong Kong following a scarlet fever death.
The second fatality comes after the illness, which mainly affects children aged between two and eight, claimed the life of a seven-year-old girl last month.
Hong Kong is particularly nervous about infectious diseases following the 2003 SARS outbreak, which killed 300 people in the city and a further 500 worldwide.
The densely populated city of seven million has also seen fatalities from multiple swine flu outbreaks.
The spokeswoman said 28 new cases had been reported in Hong Kong as of noon on Wednesday, the highest number of daily new cases this year, with the total number of scarlet fever cases in Hong Kong at 494.
The health authorities did not say whether the China tally included any fatal cases.
In Macau, a short ferry ride from Hong Kong, 49 people have contracted the illness but there are no fatalities so far this year, according to Macau health
authorities.
Scarlet fever symptoms include fever, sore throat, rashes and a "strawberry coloured" tongue, and usually subside within 48 hours with appropriate antibiotic treatment.
