The sides are due to play each other at Wembley on Armistice Day, 11 November, and both associations have said their players will wear black armbands bearing poppies.
This goes against Fifa laws which state that players’ equipment should not carry any commercial, political or religious messages.
World football’s govening body has the power to fine national associations or even dock points if its rules are broken.
However, Stewart Regan, the SFA chief executive, says the players will wear poppies.
“We think that Fifa is misinterpreting the rules and we would be prepared to challenge that,” Regan told Radio Scotland.
“It’s not a political statement.”
On Armistice Day in 2011, Scotland players wore poppies on armbands and on their tracksuits in a match against Cyrpus, with the approval of Fifa.
Regan said that he had discussed the wearing of poppies with the International FA Board: “Yes, we’ve discussed it within the International FA Board. Let’s not forget that Scotland and England are founding members of the International FA Board, the body that actually manages the rules, the laws in football.”