Aubameyang joined the Gunners from Borussia Dortmund in a £56 million ($79 million, 63 million euros) switch on Wednesday, but may be forced to sit out Saturday’s visit of Everton.
“Aubameyang was sick, so we will assess him,” said Wenger on Friday.
Arsenal are hoping Aubameyang can reignite his prolific partnership with former Dortmund teammate Henrikh Mkhitaryan, who also joined from Manchester United last month as part of the deal that took Alexis Sanchez to Old Trafford.
An unusually busy transfer window for Wenger also saw Olivier Giroud join Chelsea, while Theo Walcott could quickly come back to haunt the side he played with for over a decade when he returns to the Emirates in an Everton shirt.
Out-of-favour Chelsea striker Michy Batshuayi also joined Dortmund to complete a striker swap triangle between the two London sides and the German giants.
“It was difficult because of course Dortmund needed a replacement,” added Wenger on the drawn-out deal for Aubameyang.
“It was a cryptic deal because Giroud went to Chelsea and Batshuayi went to Dortmund. That is why it was short in time and tense until the end.”
A frantic few days was rounded off when German playmaker Mesut Ozil ended speculation over his future by signing a new three-year deal on Thursday.
“Many predicted Ozil would not commit but it is good news for Arsenal,” said Wenger.
“The fact you can keep a player of that calibre is good news.”