Gareth Southgate's side are close to securing qualification to this summer's World Cup and they will face Slovenia and Lithuania during next month's round of international fixtures.
England made one big step towards Russia after securing a 2-1 win against second-placed Slovakia in September, although the victory was slightly overshadowed by Alli's offensive gesture made on the pitch at Wembley.
The 21-year-old was showed to be swearing shortly after a collision with Slovakian defender Martin Skrtel, but the player was quick to stress that the gesture was aimed at team-mate Kyle Walker, rather than any of the officials or Slovakian players.
FIFA still decided to open disciplinary proceedings over the incident and will decide if Alli will face any punishment by Thursday, the same day in which Southgate will name his latest England squad.
A FIFA spokesperson told Press Association Sport: "We can confirm that this case will be on the agenda of the Disciplinary Committee which is scheduled to meet on 27/28 September.
"The decision will be communicated in due course; please note that disciplinary decisions are usually notified and communicated a few days after the hearing."
The football governing body could hand Allie a ban and/or a fine for the incident.
If a lengthy suspension was handed out to the 21-year-old, he could miss the start of the 2018 World Cup, should the Three Lions qualify, which they are more than likely to do.
The FA reportedly responded to the incident by sending FIFA a plea which included video evidence showing that the gesture was aimed at Kyle Walker.