The full-back previously played 178 games for the club between 2010 and 2014.
Having joined Harriers from AFC Telford United back then, he has since gone on to feature in the Football League for Cheltenham Town before making the switch to Tranmere.
He made more than hirty-five appearances for Rovers last term on his way to securing his place in the National League team of the year.
His end to the season was dealt a huge blow however; in April, he suffered a broken leg during a fixture.
Typically tenacious, though, he’s recovering superbly and is expected to return to action in September.
Vaughan had been offered new terms with Tranmere but that Harriers have reached an agreement with the 30-year-old that will keep him at Aggborough for the next two seasons.
Chairman Colin Gordon told the club`s official website: “Lee’s experience and pedigree is unquestioned and we’re delighted to secure him.
“He’s made great progress with his recovery and we’ll keep working him hard on that front, and I don’t see this as a gamble at all – he’s absolutely itching to get going and is really excited to be here.
“The manager has been very clear about wanting to bring in players who can lead on the pitch and Lee is someone who will certainly do that for us”.