The west London airport said in a statement that “out of respect” for the mourning period it will be making “appropriate alterations to our operation”.
These include flights being disrupted between 1.50pm and 3.40pm on Wednesday to “ensure silence over central London as the ceremonial procession moves from Buckingham Palace to Westminster Hall”.
British Airways has cancelled 16 short-haul flights due to the airspace restriction.
More flights are expected to be axed during the Queen’s funeral on Monday.
“We anticipate further changes to the Heathrow operation on Monday September 19, when Her Majesty’s funeral is due to take place, and will communicate those in more detail over coming days.
“We apologise for the disruption these changes cause, as we work to limit the impact on the upcoming events.”
The Civil Aviation Authority has also imposed a restriction on airspace over central London which bans aircraft – including drones – flying below 2,500ft between September 9-19.