Vaughan started his career at Liverpool, playing reserve and youth football. However, he was released in 2004 having played over 70 reserve games. He represented England at Under-15, Under-17 and Under-19 level.
At the start of the 2006-07 season, he was made Chester's captain at the young age of 21. He made 58 league appearances. On January 3 2007, new Rochdale manager Keith Hill made Vaughan his first signing, initially on loan until February 4, with a view to a permanent deal. However, on January 18 2007, Boston United signed him on a one-year contract from Chester City. He made seven appearances for the Pilgrims before rupturing his achilies tendon against Hartlepool, which sidelined him for nine-months. Now fully recovered, he rejoined Chester on February 8 2008. He was then loaned out to Droylsden for one-month, as part of a rehabilitation programme.