The 24-year-old left-back, Priestfield's Player of the Year last season, was soon to be out of contract but has committed himself to the Gills until 2015.
"Last season Joe was quite simply outstanding," boss Martin Allen told the club's official website.
"To be voted by your own team-mates as the Player of the Year must be a great feeling and to be voted as the best left-back in the division, by the opposition, is quite simply amazing.
"As a person he is conscientious, hardworking, dedicated and has a desire to play higher. He has all the attributes, on and off-the-field to get better and better."