The club's League Two status was secured under Hendon's stewardship with four games to go of the current season after their 1-0 win at Bournemouth on 11 April.
The Bees are currently unbeaten in six games and have only lost once at Underhill in 11 games since Hendon took over.
Chairman Tony Kleanthous said: "He has been a great captain for this club and a great coach. He started in his present role in an acting capacity and steadied the club during a difficult period.
"When I saw how Ian had motivated the team there was never any doubt in my mind that he was the man for the job. I expect him to go forward to big things in the game."
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