The four-week-old baby swan was attacked by a group of children at a pool in Battlefield, Shrewsbury, on Thursday, the RSPCA said.
A spokesperson said reports suggested he was "thrown around and kicked" before the nest was set on fire.
Fran Hill, from Cuan House Wildlife Rescue in Much Wenlock, where the cygnet was being cared for, said he probably had internal injuries.
"We are all devastated, we had hoped there would be a chance but if there are internal injuries we have no way of knowing," she said.
Ms Hill said the swan's mother and the remaining cygnet are still on the pool.
"The family [of swans] have suffered terribly this year - she lost her mate in April after he had to be put to sleep following a dog attack."
The police and the RSPCA are investigating who was responsible for Thursday's attack, she said.
A cygnet rescued after a suspected arson attack on his nest has died.