In 2016, he was convicted of perverting the course of justice in relation to the murder of a Liverpool police constable, and served a custodial sentence.

He was soon signed by League Two side Chester City, which was owned by his father Stephen Vaughan Sr., under the guidance of Mark Wright.

On 3 January 2007, new Rochdale manager Keith Hill made Vaughan his first signing, initially on loan until 4 February, with a view to a permanent deal.

Stephen made his first league appearance back for the club in a 5–1 win over Barnet on 30 August 2008, playing the full 90 minutes along with his brother, James.

At the present (2023) He has returned to Malta and has been elected president of the pioneers St. George's F.C in the city of Cospicua (founded 1890) On 4 November 2016, it was announced that Vaughan had been appointed as full-time director of football at Welsh Premier League side Bangor City having already been working in the role on a part-time basis from 1 August 2016.

On 26 April 2018 the FAW Club Licensing Appeals Body decided to revoke Bangor City's Tier 1 and UEFA license due to not meeting financial criteria [8] meaning that they would automatically drop down to the second level of Welsh football the next season and would not be able to compete for a place in the following season's Europa League.

[15] He is the son of former football chairman, and fellow boxing promoter and criminal Stephen Vaughan Sr.

He was charged with and convicted of perverting the course of justice in relation to the murder of Neil Doyle, a Liverpool police constable.