The Potters face a crucial Premier League meeting with Sunderland three days after their trip to Stamford Bridge, but Hughes insists that he is keen for his team to put together a long cup run.
"I will go into Sunday's game with the intention of being strong, and seeing where that takes us," he told reporters.
"We have got to be mindful about the big game on Wednesday, but that said there is sufficient time for players to recover in time for that match too.
"It's the FA Cup at the end of the day and we are all desperate to progress and remain in the competition for as long as possible."
Stoke were runners-up in the 2011 FA Cup final against Manchester City.