He was substituted in the first-half stoppage time during Spurs' 4-1 home loss against rivals Chelsea after going to the ground without contact. The game ended Ange Postecoglou's unbeaten start to the season.
Maddison has three goals and five assists in 11 Premier League appearances since moving to north London from relegated Leicester City in June.
He joins a lengthy injury list at Spurs that includes Micky van de Ven, Richarlison, Ivan Perisic, Ben Davies and Manor Solomon.
"We can confirm that James Maddison has been withdrawn from the England squad due to an ankle injury," Spurs said on X, formerly known as Twitter. "(Maddison) will remain at Hotspur Way for rehabilitation with the Club's medical staff."
Second-placed Spurs, who trail leaders Manchester City by one point after 11 matches, next visit Wolverhampton Wanderers on Saturday.
England face Malta in Group C at Wembley next Friday and travel to North Macedonia three days later.
