The Switzerland international has been on the sidelines since suffering a calf injury in the Potters' 1-1 draw with Middlesbrough.
Since the opening weekend, Stoke have lost four Premier League games in a row, but they hope to get back on track in the cup.
In this morning's press conference, Bowen told reporters: "[Shaqiri has] trained the last two sessions and it's up to the manager (Mark Hughes) whether he decides to chuck him in quickly.
"He is in the squad and whether he plays or features we'll wait and see."
Stoke have conceded 14 goals in six games in all competitions so far this season, and have scored seven.