Hughes re-joined Tranmere in July 2016 from Cambridge United, having spent the second half of the 2015/16 season on loan at Prenton Park.
Hughes, who won two caps for his country in 2006, has also played for the likes of Lincoln City, Crystal Palace, Bristol Rovers, Notts County and Fleetwood Town as well as Irish sides Ballymena United and Larne.
The 32-year-old former Northern Ireland midfielder will remain at Prenton Park for the remainder of his contract which runs until the end of the season.