Thames Valley Police force said that effective from January 27, no aircraft can enter airspace up to 760 metres above the castle, within a radius of 2.3 kilometres without special permission.
"This order is an additional method to keep the community living near to this iconic location safe," the force said.
Windsor Castle is west of London, near Britain's busiest airport at Heathrow.
The Queen, 95, usually celebrates Christmas at her Sandringham estate in eastern England, but she remained at Windsor Castle this time after the trip was cancelled because of a surge in Omicron Covid infections.
The teenager was arrested on suspicion of breach or trespass of a protected site and possession of an offensive weapon. He was detained under the Mental Health Act.
Queen Elizabeth, already Britain's longest-reigning monarch, is due to celebrate her Platinum Jubilee this year to mark 70 years since her accession to the throne in 1952.
She was forced to cut back on public appearances after a health scare in October, in which she spent a night in hospital.