Coaching at the Pro Bowl this week in Orlando, Payton was asked about Brees' future on Thursday.
"He’s coming back," Payton told NFL Network's Jane Slater. "We’ll get this done.”
Payton and Brees arrived in New Orleans prior to the 2006 season. The duo has led the Saints to six playoff appearances, including their first-ever Super Bowl victory with a 31-17 win over the Indianapolis Colts in 2010.
Even though Brees originally signed a five-year contract extension with the Saints in 2016, it included an automatic void after two years making him eligible for free agency this offseason.
Brees said after the Saints' 29-24 playoff loss against the Minnesota Vikings on Jan. 14 he expected to return next season.
“It’s the same way I felt two days ago," he told reporters. "It’s the same way I felt 12 years ago. I’ll be here as long as they’ll have me."
After three straight 7-9 seasons, the Saints made their first playoff appearance since 2013 this season and won the NFC South for the first time since 2011.
Brees set an NFL single-season record by completing 72 percent of his passes in 2017 and threw for over 4,000 yards for the 12th consecutive season.