Peter Snow and Ralph Grimston met a grisly end atop York's Micklegate Bar.
The pair were last seen gazing down at passers-by in the street below. Their severed heads had been attached to spikes.
Since that gruesome day, their faces have not been seen for more than 400 years.
They will be given a proper burial later this month.
The unfortunate men were arrested in Yorkshire in May 1598 and taken to York to be executed. Their only "crime" was Catholicism.
Four centuries later, after their skulls were found near Tadcaster, forensic experts from Dundee University have used computer software to reconstruct their faces.
Based on precise computer scans of the two skulls, academics were able to use simulation software to piece together their original likenesses.
Historians discovered Snow was a Roman Catholic priest, in his thirties, originally from Ripon, while Grimston was about 50 years old.
A month after their arrest - which took place at the height of Catholic persecution under Elizabeth I - both men were publicly executed at Knavesmire in York. Snow was hanged, drawn and quartered. Grimston was merely hanged.
Their severed heads spent several days perched on Micklegate Bar until a group of local Catholics retrieved them from their spikes and took them to Hazlewood Castle, near Tadcaster, for safe-keeping.
It was there that the skulls were unearthed during renovation work in the 19th century.
St Anne's Cathedral, in Leeds, is undergoing renovation and is due to reopen on November 13.
As part of the work, the skulls of the two men will be entombed within the altar in the sanctuary.
To mark the interment, the BBC's Inside Out programme commissioned the two computerised likenesses of Snow and Grimston. The show will be broadcast on BBC One at 7.30pm on Monday.