It will be the 48-year-old's fourth spell with the Bees, having started his managerial career at Underhill back in 2003.
He departed a year later, before having further stints in charge in 2011 and 2012.
Having been sacked from his most recent job with Gillingham in October last year, Allen has decided to accept the challenge of helping to guide Barnet back to the Football League.
"I'm really looking forward to the challenge of helping Barnet return to the Football League," he told the club's official website. "It will be great to get back onto the training pitch and work with the players ahead of Saturday's game because I have some fantastic memories of Barnet and when I've returned to the club I've always got a good reception."
Hereford United will be Allen's first opposition at The Hive on Saturday afternoon.