Klopp has previously hinted at a possible start for the 23-year-old, as Nathaniel Clyne suffered a knock to his knee in Saturday’s 5-4 win over Norwich City.
With Clyne having failed to fully recover, Flanagan is included at right-back, after a successful return to first-team action against Exeter City last week in the FA Cup.
Firmino is in strong form after having been installed as Klopp’s first-choice centre-forward in recent weeks, and the Brazilian will be hoping to add to his goal tally against the Potters.
Steven Caulker misses out as he is cup-tied for this clash, but Lovren has returned from the hamstring injury he suffered in the first-leg win over Stoke earlier this month.
Taking a 1-0 lead into this clash, Klopp will be confident that this strong, attack-minded side can seal a victory at Anfield.
Kick-off at Anfield is at 7.45pm (GMT), and is live on Sky Sports 1. Our live coverage will begin at 7.15pm.
Liverpool: Mignolet; Flanagan, Toure, Sakho, Moreno; Lucas, Can, Henderson; Lallana, Milner Firmino
Substitutes: Ward, Lovren, Smith, Allen, Teixeira, Ibe, Benteke
Stoke City: Butland; Johnson, Wollscheid, Muniesa, Pieters; Whelan, Afellay; Walters, Bojan, Arnautovic; Crouch
Substitutes: Haugaard; Bardsley, Joselu, Wilson, v.Ginkel, Adam, Shaqiri