The Welshman arrived at the Britannia Stadium prior to the 2013-14 campaign and led the club to ninth, their highest Premier League finish.
Hughes' existing deal is set to expire at the end of next season, with his stay expected to be extended until 2019.
"We are close, and there is certainly a willingness to get it completed from both sides," he said in a media conference on Friday.
"This is a wonderful club and one that matches the ambitions of myself. There's nothing I can think of to get in the way of that.
"This is a very good club. I'm happy with how it's gone and appreciative of the opportunity to be manager of Stoke City.
"It's not signed yet but hopefully it's dotting the 'i's and crossing the 't's."
Ryan Shawcross, meanwhile, has not featured for Stoke since the end of last month and Hughes says the defender has been given some time off in order to completely recover from a back problem.
"He's having a bit of time away from the club, resting," Hughes said.
"We're reasonably happy but we feel now he would be best served with complete rest rather than aggravating the back. The key is that we try to avoid an operation.
"We don't think we're at the point to make a decision on that. We're hoping this period of rest and recovery will help.
"We aren't putting a time-scale on it because everybody is different. He certainly won't be available for the two forthcoming games [against Hull City and Everton]."
