The Gunners currently top Group F with six points from their opening two matches, while Vitoria are winless and bottom of the pool after losing two in a row without scoring.
Arsenal will be looking for a big response to their disappointing 1-0 defeat against Sheffield United on Monday.
Although the North London club have been somewhat inconsistent in the Premier League this season, winning just two of their last five, their much-rotated team has been highly impressive in the Europa League, scoring seven goals and keeping two clean sheets.
The Brazilian striker Martinelli has scored four goals in his first two starts for Arsenal, and his prowess in the air will likely be demonstrated again on Thursday against a Vitoria side that have struggled to defend crosses and set pieces this season.
With that in mind, Scottish defender Kieran Tierney's penchant for attacking down the left means that he is likely to also have a strong impact on the game at the Emirates.
Statistically, the odds certainly appear to be in the Gunners' favour.
Arsenal have won their last six at home in the Europa League, their longest winning streak in European competition since they won seven in a row between March 2001 and February 2002.
Emery's side have also triumphed in four of their last five meetings with Portuguese opposition, scoring 17 goals in the process.
Recent form: WW
Recent form (all competitions): WWDWWL
Vitoria de Guimaraes
Thursday's game is Vitoria's first ever meeting with Arsenal and their first game against English opposition since the 2008-09 season when they were eliminated from the UEFA Cup by Portsmouth.
Ivo Vieira's men came through three playoff rounds to make it to this stage, but they failed to score in their opening two group games and more worryingly they are without an away win in their last seven European matches.
Although they have struggled for form of late in this competition, they have won three in a row in the Portuguese league, where they currently sit fourth in the table.
Vitoria's poor start to the group puts greater emphasis on trying to get something from Thursday's game, but their plans will be affected by an injury crisis which could see them without as many as nine first-team players.
With those absentees in mind and Vitoria's future in this competition potentially on the line, Vieira is likely to opt for a more conservative approach that allows his side to sit deep and work a low block.
Given Arsenal's recent defensive struggles, Os Vimaranenses will fancy their chances of getting opportunities in the right areas for the likes of Edwards, Davidson and Leo Bonatini.
Recent form: LL
Recent form (all competitions): LWDWLL
Emery is likely to opt for the same approach he has in previous Europa League games this season, with the club's young players and those looking for full fitness given the opportunity to impress.
Vieira is without a number of his leading names for Thursday's trip to North London.
Arsenal possible starting lineup:
Martinez; Maitland-Niles, Holding, Mustafi, Tierney; Torreira, Ceballos; Pepe, Willock, Saya; Martinelli
Vitoria de Guimaraes possible starting lineup:
Jesus; Soares, Tapsoba, Pedrao, Hanin; Edwards, Poka, Agu, Costa, Davidson; Bonatini
Head To Head
Thursday's match is the first between Arsenal and Vitoria de Guimaraes.
The Gunners have a strong recent record against Portuguese opposition, beating the likes of Porto and Braga in Champions League and Europa League games.
Vitoria, meanwhile, have won just one of their previous seven matches against English teams in European competition and that came against Aston Villa in 1983.
We say: Arsenal 3-0 Vitoria
Arsenal are likely to find their Portuguese opponents difficult to break down in the early going but they should have enough pace and quality to make it three wins from three in this year's Europa League group stage.