The midfielder completed the game, which Arsenal won 2-1, but felt an issue with his hamstring after full time.
Elneny is now being assessed by Arsenal’s medical team as they look to learn how severe the injury is.
The Egypt international is, however, expected to miss Wednesday’s game against Aston Villa at Emirates Stadium.
The injury is a blow as Arsenal are already without fellow holding midfielder Thomas Partey, who has a thigh issue.
The Ghana international is currently being monitored by physios but there is some hope he could return in weeks as opposed to months.
Oleksandr Zinchenko also missed Saturday’s win over Fulham due to a knee injury, but he is making good progress.
The Ukrainian underwent a late fitness test before that game and he is hoping to make the squad that faces Villa.