"We are of course giving extra support to the other young people we care for at this difficult time.
"Our thoughts are with his family and friends and on behalf of the staff and management we wish to express our sadness at this distressing news."
Hillcrest said it was not providing any "further details", but it is understood the boy was found hanged.
Dyfed Powys Police confirmed it was investigating the incident, which was not being treated as suspicious.
Welsh Liberal Democrat leader Kirsty Williams, who is also an Assembly Member for Brecon and Radnorshire, said: "It is a sad loss to the family and school friends of the pupil of Hillcrest Pentwyn School. Our thoughts and sympathies are with them during this difficult time."