Arsenal travel to Newcastle on Sunday to begin their domestic campaign against Steve Bruce’s side.
Pepe, who joined Arsenal for a club-record £72m fee, had been granted additional leave following his involvement in the Ivory Coast’s Africa Cup of Nations campaign.
As a result, he has had less time in first team training and did not play in Arsenal’s 2-1 defeat against Barcelona on Sunday evening.
The Gunners boss said Pepe will increase his workload in training each day, but could not guarantee whether he will feature at the weekend.
"Tomorrow, we are going to train together," Emery said. "Each day for him [Pepe] and for us is information we can save. We hope he can be [ready] for this match. With him, I want to be patient.”
Alex Iwobi and Mohamed Elneny were also late to report to pre-season due to international commitments.
"He [Pepe] is in the same situation as the other players who have been coming in the last days. For example, Lucas, after one week of training today has his first ten minutes. With Pepe it is the same. It's better to be training and be working with us."
Alexandre Lacazette has been a regular feature in Arsenal’s pre-season matches, but was missing from the match at the Camp Nou due to an ankle injury he picked up in the Emirates Cup defeat against Lyon.
Emery said the club are hopeful that he will play at the weekend.
“Hopefully he will be ready for the match against Newcastle,” he said. “The doctors are optimistic and we are going to wait. If he is okay for Sunday, perfect. If not, for the next [match].”
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