Meanwhile, the Spanish team took part in an eight-goal thriller during their opening match of the competition, winning 5-3 against Sivasspor.
Despite their disappointing defeat, Gurban Gurbanov's men sit third in Group I, currently above Sivasspor on goal difference.
In the Azerbaijan Premier League, they are also struggling - having picked up just two wins in their opening six games.
On Sunday, they only managed a 0-0 draw against Zira FK, with the Horseman currently sitting fourth in the table.
Villarreal will undoubtedly be the favourites heading into this match, with Unai Emery's team already managing a win in their first game of the competition against Sivasspor.
However, it was not without its difficulties, as the Turkish side managed to equalise twice against the Yellow Submarine during the 90 minutes - forcing the hosts to score two late goals to secure the win.
Emery's men have endured a pretty mediocre start to La Liga, despite currently sitting fourth in the table - winning three games, drawing once and losing a further three.
Their most recent league result featured a 0-0 draw against newly-promoted Cadiz, with Alvaro Cervera's side proving to be dark horses this season.
In fact, Cadiz had the biggest chance of the game as Alvaro Negredo's effort was ruled offside by VAR in the first ten minutes, resulting in a dull afternoon for both sides.
Qarabag FK Europa League form: L
Qarabag FK form (all competitions): DLWWDL
Villarreal Europa League form: W
Villarreal form (all competitions): DWWDWL
Gurbanov may opt for the same team that faced Maccabi Tel Aviv, with the visitors narrowly missing out on a point in their first game of the competition.
With both Filip Ozobic and Abdellah Zoubir scoring in the Europa League play off against Polish side Legia Warsaw, the Azerbaijan coach will be hoping his attacking players can do the same in the upcoming game.
Villarreal, on the other hand, will have to deal with a few injuries as they head into their next Europa League game.
The Yellow Submarine will be without key player Dani Parejo, with the 31-year-old set to return next month after picking up a muscle injury in their 2-1 win against Valencia.
As Paco Alcacer scored twice off the bench against their last opponents in the Europa League and started in their latest league match against Cadiz, he may be included in the starting XI come Thursday.
Qarabag FK possible starting lineup:
Mehemmedeliyev; Medvedev, Guseynov, Medina, Huseynov; Qarayev, Andrade, Matic; Ozobic, Kwabena, Zoubir
Villarreal possible starting lineup:
Rulli; Pena, Foyth, Albiol, Costa; Kubo, Coquelin, M.Trigueros; Chukwueze, Alcacer, Baena
We say: Qarabag FK 0-2 Villarreal
Qarabag have failed to score in their previous two games, so a match against Villarreal will be a particularly tough test for the hosts and we expect the visitors to claim a comfortable win on Thursday.