The 10-year-old, trained by Sandy Thomson and was a 66/1 shot to win the Grand National, was put down at Aintree after falling at the first fence.
Hill Sixteen’s death came after Dark Raven was put down following a fall in the third race during Saturday’s event.
On day one of the Grand National meeting on Thursday, Envoye Special was the first horse to suffer a fatal injury after a fall at a fence in the Foxhunters’ Chase.
A statement from The Jockey Club read: ‘Sadly, while racing in the Grand National, Hill Sixteen sustained an unrecoverable injury. Our sincere sympathies are with connections.
‘Recite A Prayer and Cape Gentleman were assessed on course by our skilled veterinary staff and walked onto the horse ambulance for further assessment in the stables.’
The Grand National main race was delayed by 15 minutes after animal rights protestors gained access to the Aintree racetrack.
Merseyside Police later confirmed that 118 arrests were made in relation to the protests.
‘There were significant numbers. I can confirm a total of 118 people have been arrested today in relation to both criminal damage and public nuisance offences,’ Merseyside Police Assistant Chief Constable Paul White said.
The 118 arrests also includes the protestors who glued themselves to the M57.
Meanwhile, the two deaths at the Grand National on Saturday have added to calls for the event to end.
‘Jump racing must be banned to prevent the brutal horrors seen today at Aintree and this week, from happening again,’ said Dene Stansall, a horse welfare consultant for Animal Aid.
‘Innocent race horses’ lives taken from them in the name of entertainment and gambling.
‘Aintree, the worst of all racecourses, is a disgrace and the Jockey Club and British racing should hang their heads in utter shame at what we have seen over the past three days.’