The 26-year-old, Orient's longest-serving player, has committed himself to Brisbane Road until the summer of 2017.
Cox was one of the O's star performers last season, scoring 17 goals in 56 appearances including one in the play-off final defeat by Rotherham at Wembley.
He wrote on Twitter: "Delighted to have signed a new deal with the club. Looking forward to being part of hopefully more success in the future."
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