Gareth Southgate's side host their neighbours at Wembley on Armistice Day in a World Cup qualifier.
A report in the Sun claimed Fifa had banned the two teams from displaying poppies on their shirts during the game as political statements are not allowed.
In 2011, Fifa eventually backed down after threatening to ban the England team from wearing poppies in a friendly against Spain, allowing them to display the symbol on black armbands.
An FA statement read: "We are working closely with the Royal British Legion once again this year to honour and remember the sacrifices made by those serving in the armed forces.
"In recent weeks, the FA has led remembrance discussions with FIFA to allow the England team to show its support for the poppy appeal during the World Cup qualifier with Scotland."
Fifa and the Scottish Football Association were unavailable for comment.