The pupils at Birches Primary School outside Portadown are being treated and the families of both children as well as pupils and staff have received anti-biotics.
The Public Health Agency said: "This is being done as a precautionary measure and the risk to the wider public is extremely low.
The condition of the two children is not known.
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A meningococcal infection can cause meningitis or septicaemia.
The PHA said it is informed about all cases of probable or confirmed meningococcal infection and will take appropriate actions.
Upper Bann MLA Jonathan Buckley described it as an 'alarming development'.
The Upper Bann MLA said: “ I am aware of an alarming development of a serious bacterial infection effecting two children locally.
"Pupils and staff at the Birches Primary School have received antibiotic treatment. However, the Public Health Agency have advised that this is just a precautionary measure and that the risk to the public is extremely low.
"I continue to monitor this situation closely. Understandably there is a lot of anxiety among parents, given the widespread sickness filtering around local schools currently. I would advise parents to be vigilant, attentive and inform themselves of the symptoms of meningococcal infection.”
The agency said: "It is important that everyone is aware of the signs and symptoms of meningococcal disease.
Early symptoms of the disease can include:
a high temperature (fever) over 37.5C (99.5F)
a blotchy rash that does not fade when a glass is rolled over it (this will not always develop)
a stiff neck
a dislike of bright lights
drowsiness or unresponsiveness
Babies with meningococcal disease tend to be irritable when picked up and have a high pitched cry, stiff body and jerking movements.
"Should anyone develop any of these they should contact their GP or local emergency department immediately," the PHA said.