A facial reconstruction of the man, believed to have been in his fifties, has been created from the skull with the help of a forensic artist.
The skeleton, uncovered at Victoria Primary School in Newhaven, Edinburgh, has been carbon dated to the 16th or 17th centuries.
The school, which is the city's oldest primary, is near Newhaven harbour where a gibbet once stood 600 years ago.
It is thought the man could have been executed for piracy or other crimes before being buried in a shallow, unmarked grave.
The condition of the bones and location of the burial close to the water and gibbet, rather than in nearby graveyards, suggests he was killed before being displayed to act as a deterrent to other pirates, said archaeologists.
Councillor Richard Lewis, culture convener for the City of Edinburgh Council, said: "Edinburgh has an undeniably intriguing past and some of our archaeological discoveries have been in the strangest of places.
"Thanks to carbon dating techniques, archaeologists now know that the skeleton was likely to have been a murder victim - and quite possibly a pirate.
"It's fantastic that through the council's archaeology and museums service, we are able to investigate such discoveries and add to our understanding of Newhaven's heritage."
Head teacher Laura Thompson said: "The pupils think it's fantastic that a skeleton was found deep underneath their playground.
"The archaeologists will hold a special lesson with some of the children about how they have used science to analyse the remains and it will be a good learning opportunity for them."
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