Aubameyang contracted malaria while on international duty with Gabon last month and he was in hospital for two days this week.
The forward is now back at home, but he is unlikely to be fit in time for Arsenal’s match with Fulham at Emirates Stadium.
“Let’s see how he recovers,” Mikel Arteta said. “Obviously, when you get a disease like this it can take a bit for the body to feel in good condition to the extreme condition we put the body through in our sport.
“But he wants to come back very quickly, he is looking forward to being back with the team so let’s wait.”
Arteta added: “He had some rough days, he was in hospital for two days but now he is at home, he is safe and he is in good condition and ready to come back.”
In his absence, Alexandre Lacazette is likely to lead the line and captain the team once again.
The Frenchman scored twice during Thursday’s 4-0 win over Slavia Prague and Mikel Arteta may want to keep a similar team to build momentum.
The full-backs, however, could change, with both Cedric Soares and Hector Bellerin hoping to come in.
Arsenal predicted XI: Leno; Bellerin, Holding, Mari, Cedric; Partey, Xhaka; Saka, Smith Rowe, Pepe; Lacazette.
Sunday 1.30pm GMT, Sky Sports
Venue: Emirates Stadium
Referee: Craig Pawson
Arsenal squad from: Leno, Runarsson, Ryan; Bellerin, Cedric, Chambers, Gabriel, Holding, Mari; Ceballos, Elneny, Odegaard, Partey, Saka, Smith Rowe, Xhaka; Aubameyang, Balogun, Lacazette, Martinelli, Nelson, Nketiah, Pepe and Willian.
Doubts: Aubameyang (malaria), Odegaard (ankle)
Injured: Luiz (knee), Tierney (knee)
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