The crash happened on the A35 near Holmsley on Wednesday night, in a section of the New Forest normally fenced off to animals.
The 18-year-old passenger was taken to hospital with "life-threatening" injuries.
The pony died at the scene. A second pony found on the carriageway was caught and returned to the forest.
The driver and a second passenger, both 18, were uninjured. The road was closed overnight but has since re-opened.
Major roads through the New Forest National Park, including the A35, are not usually accessible to animals.
However, ponies, donkeys, cattle and pigs roam free on minor roads.
It is believed the animals may have got loose after a gate was left open by a member of the public.
The New Forest pony is classed as a rare breed by animal charity, The Rare Breeds Survival Trust (RBST).
A woman is in a critical condition after the car she was in hit a pony.