The Duke of Northumberland has asked Sotheby's to sell the material in order to restore his estate's funds.
The move comes after a storm left the Duke and Duchess with a £12 million repair bill.
The letter signed by Elizbeth orders the removal of Mary to the safety of Coventry at the outbreak of the 1569 uprising.
The rebellion, which was jointly led by Thomas Percy, the Seventh Earl of Northumberland, was meant to put Mary, Elizabeth's cousin, on the English throne.
Also among the items to be auctioned is the first book to be printed in the English language, produced from the shop of William Caxton in the 15th century.
Another prize lot is a marble statue of Aphrodite dating from between 41AD and 54 AD.
Some 80 items will be auctioned at two Sotheby's sales in July.
It is estimated that the lots will sell for a total of more than £15 million.
The Duke of Northumberland said: "Over the centuries, my family has had the extraordinary good fortune to be the custodians of many great treasures.
"We dearly hope that those that are now being sold from the collection will bring as much joy to their new owners as they have to both me and my ancestors."