A boat was being hauled up the slipway when the accident happened at about 1915 on Sunday.
The trailer became detached and hit Piran Osborne, of St Newlyn East, Cornwall, who was sitting on a wall.
The Health and Safety Executive has been informed, and an investigation into the circumstances surrounding the incident will be carried out.
The boy's eight-year-old brother, who was also sitting on the wall, was taken to the Royal Cornwall Hospital in Truro with minor injuries.
The accident happened at a 2.5m-wide public slipway outside the main harbour which is free to use and is unsupervised.
Mylor: Boat was being hauled by slipway Devon and Cornwall Police spokesman PC Baxter Provan said: "Obviously this is a tragic incident and the family of the little boy must be devastated.
"Witnesses say it happened as a boat was being connected to a vehicle to be towed away and it has somehow become detached and come down the slipway.
"The five-year-old was sitting on a wall with his brother who was also struck by the boat but received only minor injuries."
Roger Graffy, managing director of Mylor Yacht Harbour, said: "A family has been ruined and my heart goes out to them.
"We are doing everything we can to help the authorities."
Staff are still mourning the death of harbour worker Stephen Head, 42, and his wife Sheila, 39, who died in a motorcycle crash at Chacewater near Truro on 5 June.
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