Flick's side travel to Alaves on Sunday, coming off Tuesday's 5-0 home win over Swiss side Young Boys in the Champions League.
Barcelona signed Szczesny as a free agent on Wednesday after the Polish goalkeeper reversed his decision to retire and come to the team's aid following Marc-Andre ter Stegen's season-ending injury.
Barca are top of the LaLiga standings with 21 points from eight games while Alaves are 11th with 10 points.
"Szczesny is in good shape and with his experience, character and quality I think he the very best option for the club. It's very good to have him, he will help us a lot but he is not with us against Alaves," Flick told reporters on Saturday.
The Catalan side have a tough run after the international break, hosting Bayern Munich in the Champions League three days before visiting Real Madrid in LaLiga on October 26th.
"I am sure after the international break Szczesny will be an option for us. For him also, to play for Barca will be great. We will see how he is doing in training, we have a lot of time," Flick said.
Flick had said his decision to rest key starters had an impact in their first loss of the domestic season, a 4-2 loss at Osasuna last weekend, and accepted that players would be upset with his decisions.
"It's normal to get angry, everyone wants to play more. Those changes had to be made. It's a decision that they have to accept and they did," he added.
"Lamine Yamal (who started on the bench and was subbed in the 59th minute) complained that he wasn't receiving many balls, but now he can work on fixing that.
"We have to avoid the many mistakes we made at Osasuna. We need to have more control and possession. It is going to be a high-intensity game at Alaves."
