County, 21st in the table, sacked Paul Ince eight days ago and find themselves in the bottom four of the division battling for survival just one year after winning promotion following their 3-1 defeat at Dagenham and Redbridge on Saturday.
Barnet face relegation from the Football League in the bottom-two of League Two. But ex-West Ham favourite Allen, nicknamed 'Mad Dog', guided the club to a crucial 2-1 win over Crewe at the weekend and took seven points from three undefeated games.
Fight for survival: Martin Allen takes over League One strugglers Notts County at a critical stage of the season
County equalled a club record of seven successive defeats by losing 3-1 at Dagenham to drop into the League One relegation zone.
Barnet had taken seven points from a possible nine since Allen, 45, took over and are now level with third-bottom Burton Albion.
Allen upset Bees supporters seven years ago when he left the then Conference club to join Brentford, but he insists he has nothing to feelguilty for.
'Barnet are now set up to not get relegated,' he told Sky Sports News.
Lift off: Allen must guide Notts County, who played Man City in the FA Cup earlier this season, away from the drop zone in League One
'I've got to look after myself and my family and I've got bills to pay.
'County have just lost their last seven games so obviously it isn't going too well and something needs to happen. It's a tough ask.
'We'll see if we can put a team together, get the buzz back into Notts County and get some results.'
Allen's first game in charge will be at Yeovil on Tuesday night whileformer Barnet striker Giuliano Grazioli, who was Allen's assistant, hasbeen put in caretaker charge at Underhill.
All the buzz of the Football League: Tubbs fires Crawley to promotionInce's six-month reign at League One Notts County ends by mutual consentThe 2010/11 managerial merry-go-round: Allen leaves Barnet after three games
Explore more:People: Paul Ince, Martin Allen Organisations: Football League