The 35-year-old has been voted by his teammates to lead out the host nation at Wednesday's opening ceremony.
Burton, who has won three European Championship and two World Championship bronze medals, was preferred to Linda Clement (hockey), Jennifer McIntosh (shooting) and Alex Marshall (bowls), all of whom will immediately follow behind Burton.
He told reporters: "It's a massive honour and it's a big responsibility. We're often in this relatively isolated judo bubble so for Scottish athletes of all 17 sports to nominate me as flag bearer is huge.
"It's also at the very end of my career and I'm now involved in coaching a number of guys in the team which adds a completely different dynamic.
"I remember walking in behind Chris Hoy in London and experiencing that spine tingling moment when we entered the stadium. To think that I'm going to be at the front of Scotland's largest ever team and hopefully our most successful ever just blows your mind."
Burton has represented Great Britain at the last two Olympics, but this will be his first appearance at a Commonwealth Games since Manchester 2002 as Judo has only this year returned to the programme.