Vaughan has been at Oakwell for four seasons but now departs on the back of just one year working with head coach Daniel Stendel.
During his time at the club he has helped Adam Davies become one of the best goalkeepers in the club's history
Davies, who has been turned into a Wales international, is out of contract this summer, but looks set to leave for a big-money move having yet to pen terms on a fresh offer from the Reds.
He has also helped develop youngsters Jack Walton and Jake Greatorex, who signed a new deal earlier this summer.
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The club said: “Everyone at Barnsley Football Club would like to thank John for his commitment and professionalism whilst at Oakwell and wish him the very best of luck with his future career.”
His replacement has yet to be announced.
Whoever the new man is, he will have to buy into Stendel's way of working, one which proved so successful in his debut season at the club.
All the players were on board and that was a key component of the club's promotion, according to coach Dale Tonge.
He said: “They have bought into a different culture and way of training and I think it has been evident not just in training but in games especially where the boys have gone out with no fear and played some really attractive football this season.”