The agency said it is aware of seven deaths among invasive group A streptococcal infections (iGAS) cases between October 3 and December 25.
Two of the deaths were in children under 10.
The deaths of the children in Scotland are the first to be recorded north of the border, though children have died elsewhere in the UK.
The most recent data from the UK Health Security Agency (UKHSA) shows 21 children under 18 in England have died from invasive Strep A disease, while there have been a further three deaths in Belfast and Wales.
Infections caused by Group A Streptococcus (GAS) include the skin infection impetigo, scarlet fever and strep throat.
While the vast majority of infections are relatively mild, sometimes the bacteria cause iGAS, a life-threatening infection in which the bacteria has invaded parts of the body such as the blood, deep muscle or lungs.
Scotland’s Health Secretary Humza Yousaf tweeted: “Every death is a tragedy, particularly those of young children, my thoughts with families & loved ones affected.”
He added: “Thankfully most cases of Strep A present as mild illness & can be treated with antibiotics. Working with UK Govt to ensure adequate supplies.
“Where localised shortages of first line treatments occur there are alternative & effective antibiotics available.”
PHS said that in the week ending December 25 there were 869 laboratory reports of Group A Streptococcus (GAS), a reduction from 1,079 the previous week.
This compares with between 300 and 480 reports per week during peaks observed in the period since 2016.
The PHS report said: “Although increases in GAS were reported in recent weeks in Scotland, iGAS infections levels for 2022 have been generally stable and similar to previous years.”
In the week ending December 25 there were 15 iGAS cases reported across all age groups, compared with 13 in the previous week.
This compares with between 12 and 18 cases per week during peaks observed in previous years.
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Data from the beginning of October to December 25 2022 show that PHS has received reports of 20 iGAS cases in children under 10.
Health officials have urged parents and those who care for children to be vigilant, and help reduce the spread of infections by washing their hands frequently with soap and water, and covering their mouth and nose with a tissue when they cough or sneeze.
If a child is showing signs of scarlet fever, parents and carers are urged to seek advice from a health professional as most cases respond promptly to early treatment with antibiotics.
Symptoms of scarlet fever include headaches, a sore throat, high temperature and a pinkish skin rash, which feels like sandpaper to the touch.