The new deal will keep the 24-year-old at Brisbane Road until the summer of 2013.
“I am delighted Jimmy has signed for another two years,” Orient boss Russell Slade told the club’s official website.
“We didn’t want to have to replace him. He has just come off the back of a good season and hopefully he can pick up where he left off.
“If he does that then he will be a real asset to the team.”