Tim Flowers is to leave The Hive after being unable to turn around the club’s fortunes.
Arriving in December, the Bees have won once under his stewardship and have lost their last five.
On Tuesday night, they went down 2-0 at home to Wrexham - their tenth defeat in eleven National League matches.
The news came an hour after Flowers’ old club Solihull Moors and their manager Jimmy Shan parted ways.
Flowers told the club's website: “As challenging as it’s been I’ve thoroughly enjoyed my time with Barnet. It just got to a point where I couldn’t get any more out of the team.
"There are a decent amount of games left to play and certainly enough to get out of the bottom of the table and I believe things will turn but it might just need a different voice in the dressing room.
“Ultimately, we brought in some players who tried hard but it just hasn’t happened. Personally, I’d like to wish everyone at the club and all the fans my very best for the future.”
Bees chairman Tony Kleanthous said: “I would like to place on record my thanks to Tim for all of his efforts for our Football Club and wish him and his staff the very best of luck for their future endeavours.
“Ultimately, on this occasion, it just hasn’t worked out, which is disappointing because of the high regard in which I hold Tim.”
Head of Performance Gary Anderson will oversee things until the club appoint a new manager.