They follow the example of Peterbrough United who had already stated their intention to hold a minute's silence as the nearest league club to the village of Soham.
"The whole nation has been shocked and saddened by the deaths of Holly and Jessica," explained FA Marketing director Paul Barber.
"The girls love of football is well known and everyone connected to the game is keen to pay their respects to Holly and Jessica and offer their condolences to the girls' families and friends at this very sad time."
The man charged with the murder of the two, Ian Huntley, used to live in Scunthorpe before moving to Soham. He lived with his girlfriend, Maxine Carr, who also faces jail over a charge of attempting to pervert the course of justice.