Both children, aged five and six, were pupils at Millstead Primary School, in Liverpool, which teaches children aged two to 11 with special educational needs.
The UK Health Security Agency, which has been monitoring the infections, said a link between the deaths has not been established, but stressed they are "unlikely" to be due to the giardiasis outbreak.
Giardiasis is an infection of the digestive system caused by tiny parasites and typically causes symptoms such as diarrhoea and stomach cramps and is normally treated easily with antibiotics.
Devastated
The UKHSA has not said when either child died. But a letter from the school's headteacher Michelle Beard was sent out on May 21, alerting parents to two cases of giardiasis at the school.
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