The stonework was found shortly after a project to open up the castle's Sally Port for the first time since 1649 got underway.
It is thought to date back to the Civil War period, when the castle was held as a Royalist stronghold but besieged by Parliamentarian forces.
Neil Redfern, principal inspector of Ancient Monuments with Historic England, said: “Parts of these features may possibly date to the final siege of Pontefract Castle during the English Civil War in 1649. They give the real impression of a garrison working furiously to shore up the defence of the castle that had suffered considerably after three years of sieges."
The Sally Port, a controlled entryway to a fort or prison which can be used as an emergency exit in times of trouble, is being opened up as part of the Â£3.5m Key to the North project, funded by the Heritage Lottery Fund, Historic England, Wakefield Council, The Wolfson Foundation, and landfill charity Epac.
Visitors will be able to enter it for the first time, and see the newly-discovered floor, when work to the castle is completed at the end of the year.
David Renwick, head of the Heritage Lottery Fund in Yorkshire and the Humber, said: “Pontefract Castle has a long and colourful history, and has frequently found itself at the centre of national events, as a royal residence where Richard II was murdered, under siege during the Civil War, and immortalised twice in Shakespearean verse.
"This is a really exciting discovery, uncovering even more of the fascinating history of this incredibly significant site, and we’re delighted that support from National Lottery players has made it possible.”
Coun Jacquie Speight, Wakefield Council's cabinet member for culture, leisure and sport said: “This is a very exciting and unexpected find dating back to the Civil Wars.
"It’s led to a short delay on site, but a redesign that means visitors will be able to come and view the floor once conservation works are finished.”