They also confirmed that a second child who was being treated for the same illness has gotten a liver transplant.
Both of these cases have been linked to an unexplained type of hepatitis that has been appearing worldwide, with less than 500 cases.
The European Centre for Disease Prevention and Control has said that the total number is approximately 450.
An urgent alert for this first was raised in the UK in April and it has been detected in dozens of countries since, including Ireland.
Over the last two months, the HSE has confirmed six probable cases of children with hepatitis of unknown cause, all aged between one and 12 and all being hospitalised.
Also, a small number of other cases are being assessed to determine if they are linked to his acute hepatitis of unknown origin or if they have another cause.
The HSE says the cause of acute hepatitis in these children has not yet been found and they are looking into all possibilities.
One particular area being investigated is the link between this and an increase in infections caused by adenovirus, a common cause of childhood illness.
Others include infections such as Covid-19 or something in the environment.
Investigations are ongoing to determine if current or prior Covid-19 infection may cause an increase in risk of this disease in children.
None of the children tested in Ireland showed evidence of a Covid-19 infection at that time, with a majority of the cases not having received the Covid vaccine.