Archaeologists have found the skeleton of an adult man buried face down in a ditch, his hands tied under his pelvis.
The unusual burial position suggests that the Iron Age man may have been the victim of murder or execution, he added.
Osteologists are currently examining the skeleton for new evidence of foul play, HS2 said.
Other discoveries on the site cover more than 4,000 years of human history, including a circular wooden monument resembling the layout of Stonehenge.
Project archaeologist Rachel Wood said: “We already knew that Buckinghamshire is rich in archeology, but the discovery of a site showing human activity spanning 4,000 years surprised us a little.
“The death of the Wellwick Farm man remains a mystery to us, but there are not many ways to end up in the bottom of the ditch, face down, hands tied.
“We hope our osteologists will be able to shed light on this potentially horrible death.
“The large wooden ceremonial structure, the Roman lead burial and the skeleton mystery at Wellwick Farm help to bring to life the fact that people lived, worked and died in this region long before we arrived. “
Archaeological work has revealed evidence of human activity dating from the Neolithic to the Medieval period, a period spanning approximately 4,000 years, said HS2.
A large circular monument of wooden poles 65 meters in diameter with elements aligned with the winter solstice, similar to Stonehenge in Wiltshire, was also discovered as well as a skeleton in a lead-covered coffin, was -he adds.
HS2 said that the buried person must be a high-ranking person to afford to pay for such an expensive burial method.
Its lead archaeologist, Mike Court, said the finds will be shared with communities and the public through virtual lectures, open houses and an upcoming documentary.
He added: “Before building the high-speed, low-carbon train between London and Birmingham, we discover an archaeological wealth that will enrich our cultural heritage.
“The scale of the possible discoveries, the geographical extent and the vast extent of our history to be discovered make the archeology program of HS2 a unique opportunity to tell the story of Buckinghamshire and Great Britain. ”
The announcement of the discovery comes at the start of the Festival of British Archeology, an annual event that takes place over nine days between July 11 and 19, where HS2 will host digital events highlighting recent archaeological discoveries.