Professor Bennett Zon, head of music at Durham University, said the Latin version of the song, Adeste Fideles, celebrated the birth not of Jesus but of the prince.
He said: "There is far more to this beloved song than meets the eye.
"Fideles is Faithful Catholic Jacobites. Bethlehem is a common Jacobite cipher for England, and Regem Angelorum is a well-known pun on Angelorum, angels, and Anglorum, English.
"The meaning of the Christmas carol is clear:
'Come and Behold Him, Born the King of Angels' really means, 'Come and Behold Him, Born the King of the English' - Bonnie Prince Charlie!"
These are deep waters, Watson. "Even today, some Highland clans and regiments pass their drink over a glass of water during the Loyal Toast — to the King Over the Water. "