The boy was airlifted to Southampton General Hospital by a Coastguard rescue helicopter.
Immediate next-of-kin have been informed, but police will not be in a position to confirm the boy's name until all formal identification procedures have been completed, a police spokesman said.
An initial post-mortem examination will take place in the next few days.
Senior investigating officer Detective Inspector Floyd Higginson from Hampshire Police said: "Although the death is not being treated as suspicious, it is routine procedure for specialist detectives to make initial inquiries into the sudden death of someone aged under 18.
"We are providing support for the other three people on board the boat to help ensure their welfare, and to establish the exact circumstances surrounding the death."