Medical authorities said the boy was taken to hospital with a fever and died Tuesday.
In May, a 7-year-old girl became the first person to die of scarlet fever in Hong Kong in at least 10 years.
Researchers at Hong Kong University said she had a genetically mutated strain that is much more resistant to antibiotics.
Hong Kong has had 466 reported cases of scarlet fever so far this year, about double the annual total.
Scarlet fever is a streptococcal disease characterized by a skin rash. Source
"Schools Hit by Outbreak should be Closed"
The government has been urged to close all primary schools and kindergartens affected by outbreaks of scarlet fever. One child has died this month after catching the disease, which authorities say has mutated. Doctors are trying to confirm if a second child, a five-year-old who died yesterday, had also contracted scarlet fever.
The convenor of Caring Hong Kong, Dr Kwok Ka-ki, says with 450 cases so far this year, the disease has spread much faster than in previous years. Dr Kwok said he was alarmed by the fact that the bacteria appeared to be resistant to the antibiotic, erythromycin, which is often used to treat the disease.However, the Controller of the Centre for Health Protection, Dr Thomas Tsang, says it is unlikely schools will be suspended, because less than 10 percent of all scarlet fever cases have been contracted in schools. He reminded children to maintain good personal hygiene to help prevent the spread of the disease. Source