The rare bird, which had been 'adopted' by pupils at Ballyclare High School, in County Antrim, was found in the Katesbridge area in May.
The current population of red kites in Northern Ireland is thought to stand at around 14 breeding pairs.
Pupils had given the bird the nickname Fawkes and were supporting an RSPB red kite re-introduction scheme.
Teacher Adrian Witherow said: "We are extremely disappointed about what has happened to Fawkes.
"Both the staff and pupils were fully behind the red kite re-introduction scheme and it is a real shame that the bird which we have followed for a number of years has been deliberately targeted."
He added: "RSPB NI has offered us the chance to adopt a chick born this year, which will be doing to show our ongoing support for the project."
The bird was found near a nest site usually occupied by a male and female known as Black K and Black M.
Worryingly, they have not been seen in recent months and their nest, which was freshly lined in preparation for breeding, has not been active for weeks.
Claire Barnett from RSPB NI said: "To lose any of our small red kite population is a real setback, but to find out that someone deliberately killed this magnificent bird of prey is beyond belief.
Ms Barnett added: "Like all wild birds, red kites are protected by the law and it is an offence to injure or kill one.
"We would also encourage the public to keep an eye out for Black K and Black M.
"Look for the tags on the underside of the wing and report any sightings to: redkiteni@rspb.org.uk"
The RSPB Northern Ireland has confirmed that a red kite was been deliberately shot and killed in County Down.