Hughes has been with Charlton since the summer of 2011, helping them to promotion to the Championship in his first season, but he spent much of last season on the sidelines with an Achilles injury.
He returned to action in March and was a key part of the team that finished the season in fine form, and he is keen to kick off 2013-14 in much the same vein.
"I can't put into words how happy I am," Hughes told Charlton's official website after signing his new contract.
"I'm over the moon and honoured that the manager wants to keep me for another season. For him to say he wants to keep me as a player meant the deal took about a minute to conclude. It was just a 'yes' straight away.
"I feel I am very lucky to be given the chance to stay here and be a part of what he is building with his staff and to work with this group of players and the youngsters coming through."
Boss Chris Powell was equally pleased to retain a player he values as a good character in and around the club.
"I'm really pleased that Andy has agreed to continue playing with us and will be a part of our squad going forward for next season," said Powell.
"His enthusiasm has shone through since he arrived at the club. It's great for us to tie him down for another year, and hopefully we can help him to begin making the transition into the next step in his career.
"Andy played a vital role for us on the pitch over the course of the last eight of games of the season and he also has great qualities in the dressing room.
"He is a great role model for our academy players and development squad as well, as we saw last season. You cannot have too many characters like him around the club."