Pennant was set to be released this summer by former Britannia Stadium manager Tony Pulis - but the 30-year-old has since impressed Hughes.
The former Liverpool and Arsenal player has earned a new one-year contract to provide room to develop over the new season.
Hughes said in the Daily Star: "I think I can take him on.
"One of my backroom staff, Eddie Niedzwiecki, worked with him at Arsenal so he knows him well. There's a personal relationship there that we can build on and revisit.
"He will enjoy the day-to-day work we do as well, it is very player orientated. So the type of work we do on a daily basis will encourage him, I am sure.
"I needed to sit down with Jermaine and just talk to him one-to-one. I sense he still has more to give Stoke City and that he is really motivated to kick on."