French defender Koscielny ruptured his Achilles tendon during Arsenal's Europa League semi-final second-leg defeat to Atletico Madrid in May.
The injury subsequently robbed him of a place in France's World Cup-winning campaign, while he has yet to feature for Arsenal's first-team since Emery took over from Arsene Wenger.
Now 33, Koscielny has been nursed back to fitness in recent weeks thanks to appearances for Arsenal's second team, and Emery confirmed he will feature against Qarabag, with the Gunners already assured of top spot in Group E.
"Our first mind in this competition is to be first in the group - which we have done," Emery told reporters on Wednesday.
"But we respect this competition and Qarabag. [On Thursday] our objective is to win, we will give a players chance to take responsibility and confidence.
"We are going to use the match with some different players, with some coming from Under-23s. We also start to play with Laurent Koscielny."
"We have some players with injuries and unavailable at centre-back," he said. "We are going to decide after Thursday [if Koscielny plays at the weekend], because it will be the first time Koscielny can play.
"We can use other players in this position, like sometimes [Nacho] Monreal and [Stephan] Lichtsteiner, so we will decide, but first we think about the Qarabag game."
Mesut Ozil is also in contention after four games out with a back injury, though Emery gave little away about whether he will start or be on the bench.
"He is in the group, we will decide if we play at the beginning or during the match," Emery said.