On 20th July 2005, Norwich agreed terms with Reading for their versatile right-sided midfielder Andy Hughes paying the Berkshire £500,000. The Reading website describes him as "energetic and gifted" and he can play anywhere across midfield or even at full-back. Hughes played 46 games in 2004/5 scoring once.

He began his career with Oldham, making 44 appearances, scoring once, before joining Notts County, initially on loan and then permanently on 23rd March 1998. He made 130 appearances for the Magpies, scoring eighteen goals. He moved to Reading in July 2001 for £150,000 making 183 appearances for the Royals for whom he scored 19 times.

Andy made his debut for Norwich in the 1-1 draw with Coventry on the opening day of the 2005/6 season.

Andy's performance in midfield made him a taregt for the Carrow Road boo-boys but performances at rightback at the end of the 2006/7 season saw him gain more approval. In June 2007, more than one national newspaper linked Hughes with a switch to Leeds once they had come out of administation and were allowed to start purchasing players again.Manager Dennis Wise is understood to be genuinely interested in the former Reading man. This materialised on 9th August 2007 with Andy signing a two year deal for an undisclosed sum.

Peter Grant told Norwich's official website: "Andy did exceptionally well for us last season but with John Otsemobor coming in it was always going to be tough for him this season. Leeds were able to offer him a longer deal which I didn't feel able to do. Andy is a fantastic person who we're sad to lose. His quality of character shone through last season and it was therefore not right to stand in his way."

Andy signed for Scunthorpe on 21st January 2011 on a free transfer. The 33-year-old, whose Leeds contract was going to expire this summer, has signed an 18-month deal with the option of a further year. He had made 139 appearances for Leeds. Unfortunately for Hughes, and teammate Michael Nelson, Scunthorpe were relegated to League One on 30th April 2011 following a 5-1 defeat to Notts Forest.

Andy joined Charlton on 1st August 2011 on a free transfer, signing a two year contract. He joins fellow former Canaries Gary Doherty, Paul Hayes and Rhoys Wiggins at the Valley. Charlton won promotion to the Championship on 15th April 2012 with a 1-0 win at Carlisle. The following week, it was confirmed that they had won the League One title.

On 7th May 2014, it was announced that Hughes would be leaving Charlton when his contract expired in June 2014. He had played 34 games for Charlton.

Andy signed for Bolton Wanderers on 21st July 2014 as player-coach. The 36-year-old will work as a professional development coach with Bolton's under-21 and academy sides.

On 11th December 2015, Andy left Bolton to become first team / development coach at Rotherham. He said "I have been lucky enough to have worked as an academy coach with the under-21s at Bolton, but the opportunity arose to come here and create something which is very exciting, The role will see me working closely with the academy and first team."

Hughes was released by Rotherham along with manager Neil Redfearn in early February 2016, On 3rd March 2016, he joined Crystal Palace as first team coach, teaming again with Alan Pardew who was his manager at Reading.

Andy was appointed as first team coach at Huddersfield on 26th May 2016 and he played an instrumental role supporting David Wagner as the Terriers won promotion to the Premier League in May 2017, returning to the top flight for the first time since 1972. The following season saw them finish a respectable 16th place.When David Wagner left Huddersfield by mutual consent in January 2019, Hughes stopped working with Huddersfield on a day-to-day basis and his departure, along with that of assistant head coach Christoph Bühler, was officially confirmed at the end of the 2018-19 season upon Huddersfield's relegation from the Premier League

On 21st August 2019, he was appoitned as Under-23s' lead coach at Sheffield United. He later had a role working under Garry Monk at Sheffield Wednesday.

On 25th June 2021 it was reported that he was joining the Canaries for pre-season on a temporary basis believed to include coaching the group of players City hope to send out on loan next season. His remit is understood to include monitoring the group of players who are not in Farke's plans and searching for new opportunities with 12 months remaining on their contracts. This was made permanent when the current Loans Manager Neil Adams was promoted to the role of Assistant Sporting Director at the end of September 2021.

On the appointment of David Wagner as Norwich's manager on 6th January 2023, Hughes was promoted to first-team coach having worked with Wegner at Huddersfield.

Rumours in late June suggested Andy would/had quit Norwich to become part of Steve Cooper's coaching team at Leicester, newly promoted to the Premier League. His departure to Leicester was confirmed on 8th July 2024. “Despite all being disappointed that we’re losing such a key member of the team in Andrew, he leaves with our very best wishes," said sporting director Ben Knapper

After Steve Cooper was sacked in November 2024, Hughes would support caretaker manager Ben Dawson.