The 51-year-old's appointment as Tony Pulis' successor in 2013 led to demonstrations from some Stoke fans.
But Hughes guided Stoke to their best Premier League finish - ninth - in 2013-14 and they currently lie 10th.
QPR sacked Hughes in 2012 as they headed for relegation to the Championship.
The Welshman is unsure about speculation he will be given an additional two years.
"The length and terms will be discussed in due course I would imagine," he said. "But I'm delighted they want to do it."
The Coates family who own the majority of Stoke's shares, and Chairman Peter Coates have a record of sticking with their managers, with only 3 in the last 11 years.