Buns have traditionally been thrown from the top of the building since the coronation of George III in 1761.
The event had previously been put into doubt because of renovation work on the Grade I listed building.
Adela Thomas, of the museum, said people would have to throw "a little further" to clear the scaffolding.
The tradition celebrates royal weddings and significant anniversaries.
The buns, which are baked locally, were thrown to mark the Queen's Golden Jubilee in 2002 and for the 450th anniversary of Abingdon's town charter in 2006.
The Mayor of Abingdon and members of the town council will take part in the event.
Ms Thomas said: "We've been assured that people will have access to the roof. Four thousand currant buns will be thrown to the waiting crowds below.
"Recent... occasions have witnessed bun throwers using novel ways of propelling the buns including the use of tennis racquets and catapults."
The roof and interiors of the County Hall Museum are currently being renovated as part of a Â£3.5m Heritage Lottery Fund project.
When it opens in May 2012 it will have increased display areas, a cafe and a learning community space.
The bun-throwing begins at 1800 BST on Friday 29 April.
Thousands of currant buns will be thrown from the roof of the Abingdon County Hall Museum to mark the marriage of Prince William and Kate Middleton.