Orient manager Russell Slade was delighted to tie down the striker following his most successful scoring season last time out, netting 13 times.
"Mooney enjoyed his best season with us last year and scored some really important goals," Slade told Orient's official website. "If he hadn't got injured towards the end of the year I'm sure he would have scored a few more too.
"It's great to get him tied down with a new contract as, for the way we play, he fits perfectly into the make-up of the team."
Mooney has made 84 appearances overall for the club.