First team opportunities at Richmond Park became difficult to obtain for Hughes resulting in his departure on loan to First Division Kilkenny City during the 2001–02 season.

[citation needed] Hughes departed St. Pats at the end of the 2002–03 campaign, to join Kildare County for the first summer soccer season of 2003.

It was a difficult season for Hughes as scored just three goals in 20 appearances for the struggling Vikings, and he was initially released along with 14 other players by new Dublin City manager Roddy Collins in a mid-season cull.

[8] He scored eight goals in 25 appearances that season for Monaghan United before joining his former manager at Kilkenny, Kildare and Dublin City, John Gill at First Division promotion chasing Dundalk.

Hughes made his Dundalk debut on the first day of the 2006 League of Ireland First Division season in a 2–1 defeat away to Shamrock Rovers at Tolka Park on 10 March 2006.

Hughes was released by Dundalk immediately after the conclusion of the 2007 season, but he did not wait long to find a new club when he joined Shelbourne on 29 November 2007.

[14] Hughes was given the number 27 shirt and made his first appearance since his return to the club on 4 July, in the Europa League away to Žalgiris at the LFF Stadium in Vilnius, Lithuania.