Osteologists are now examining the bones for signs of foul play.
Dr Rachel Wood, the project archaeologist, said: “We already knew that Buckinghamshire is rich in archaeology but discovering a site showing human activity spanning 4,000 years came as a bit of a surprise to us.
“The death of the Wellwick Farm man remains a mystery to use but there aren’t many ways you end up in a bottom of a ditch, face down, with your hands bound.
“We hope our osteologists will be able to shed more light on this potentially gruesome death.”
Archaeologists have discovered in a square enclosure at the site a skeleton buried in a coffin lined with lead.
The outer layers of the coffin were likely made of wood and its occupant would have been someone of high status.
Dr Wood said: “The large wooden ceremonial structure, the Roman lead burial and the mystery of the skeleton at Wellwick Farm helps bring alive the fact that people lived, worked and died in this area long before we came along.”
The announcement comes at the start of the annual Festival of British Archaeology, from July 11 to July 19.
During the festival, HS2 will host digital events to showcase recent archaeological discoveries.
Mike Court, HS2 Lead Archaeologist, said: “Before we build the low-carbon high-speed railway between London and Birmingham, we are uncovering a wealth of archaeology that will enrich our cultural heritage
“Our discoveries will be shared with communities and the public through virtual lectures, open days and in an upcoming BBC archaeology documentary.
“The sheer scale of possible discoveries, the geographical span and the vast range of our history to be unearthed makes HS2’s archaeology programme a unique opportunity to tell the story of Buckinghamshire and Britain.”
HS2’s archaeology programme is part of Phase One the rail project – London to Birmingham.
This section of HS2 is being prepared to build the Wendover Green Tunnel and the Wendover North Cutting.