The 1,585cc Dyna Super Glide was given given to the pope in June to mark the 110th anniversary of the US motorbike maker, London-based auctioneer Bonhams said.
The bike, which is signed by Pope Francis on the petrol tank, is expected to fetch between USD 16,400 and USD 20,500 when it goes on sale at the Grand Palais in Paris on February 6.
The pope donated the Harley in November to the Roman Catholic charity Caritas Roma and the funds from the sale will go towards the restoration of its Don Luigi di Liegro hostel and soup kitchen based at Rome's Termini railway station.
"We hope to be able to do both Pope Francis and Harley-Davidson proud by raising a significant amount of money for a very worthy cause."
Pope Francis, 77, is not thought to have ridden the Harley, a make well known for its use by motorbike gangs including the "Hells Angels".
The famously humble pontiff is more of a fan of buses. He opted to ride one the day after his election last year instead of taking a limousine, and regularly used them in his homeland Argentina instead of taxis.