Barça moved to the top of La Liga with Saturday's 3-1 defeat of Alaves, although Atletico in fourth are only three points back. Pedri made his first team return as a second-half substitute on Saturday after more than a month out with a hamstring problem.
He is in line to start against Diego Simeone's rugged outfit, as is midfield partner Frenkie de Jong, who missed the Alaves match for family reasons.
"I'm really happy. The players are coming back, maybe we can increase our level. This is the most important thing," Flick said on Monday, although he confirmed that Uruguayan centre-back Ronald Araujo is out.
The German has come under fire this seen for a series of abject displays, not least in the Catalans' highest profile matches - a 3-0 defeat to Chelsea and 2-1 reverses against Real Madrid and Paris Saint-Germain.
Despite being top of the table, Flick admitted that Barça need to improve.
"I know we are not (in) top (form) like last season," he said. "But we have potential. And we have to increase our level."