The remains are of a young man dating from the 12th or 13th centuries, at the site of Kirk Ness, a church and cemetery in North Berwick, East Lothian.
He was fatally stabbed four times in the back, twice in the left shoulder and twice in the ribs.
The archaeologists said he was aged over 20, of slightly better build than average, and had wear to the shoulder, which suggests he might have been an archer.
The dig was organised by the Scottish Seabird Centre, which is now on the site, and Historic Scotland. It also revealed structural remains including stone tools, lead objects, ceramic material and bones of butchered seals, fish and seabirds, which suggest a community lived at the site.
The centre's chief executive, Tom Brock, said: "Being at the centre of a 900-year-old murder mystery is very exciting for the Scottish Seabird Centre.
"As an independent visitor attraction, conservation and education charity, we are dedicated to inspiring people to enjoy, protect and learn about their local environment, and this dig has allowed us great insight into how life was lived in the North Berwick area almost 1000 years ago.
"The site of the centre is a historic site of national importance and visitors can find out more about this rich history from information displayed within and around the Seabird Centre."
Archaeologists uncovered various graves at the site during the dig, which was prompted by the expansion of the centre.
By assessing the size, shape and relative positions of the injuries to the bones of the murdered man, they surmised that the dagger-like weapon used to stab him had a symmetrical lozenge-shaped section with very sharp edges and was probably at least 2.75 inches long. Archaeologists said daggers with a lozenge-sectioned blade were a specialist military weapon and that this, combined with the accuracy of the stab wounds, implied a degree of professionalism in the killing and arguably a degree of calculation.
The bones may be re-interred in the cemetery.
The dig was carried out by Edinburgh-based Addyman Archaeology, with work undertaken between 2000 and 2006 followed by scientific analysis.
The findings of the Kirk Ness project have been documented in a new book, The Medieval Kirk, Cemetery and Hospice at Kirk Ness, North Berwick.
Rod McCullagh, senior archaeology manager at Historic Scotland, said: "These archaeological discoveries mark a significant advance in our understanding of the early history of North Berwick."