1990s

A good run in the 1990-1 FA Cup (Clapton, Braintree, Harlow, Heybridge Swifts, Chelmsford City and Northampton Town) culminated in a home defeat by Portsmouth in the 3rd round. Coming up to April 1991 the conference table was close; Barnet, Colchester, Kettering Town and Altrincham all in with a chance. The last game of season 1990-1 finally saw Barnet in the 4th Division.

Season 1991-92, the first season in League Division 4, the club finished a very creditable 7th and just missed being promoted in the playoffs after beating Blackpool at home 1-0 but succumbing to a 2-0 defeat in the away match.

In Season 1992-93, the old Division Four was re-designated Division Three on formation of the F.A. Premiership. The club had a successful campaign finishing 3rd and promotion to Division Two.

Division Two however proved a much more difficult task, the club losing 28 games in season 1993-4 and returned back to Division Three. A rare highlight in the season was 0-0 draw against Chelsea at Stamford Bridge (FA Cup 3rd round). Queens Park Rangers inflicted a 6-1 aggregate Defeat in the Football League Cup.

For the next seven seasons, Barnet maintained a position the League Division Three. There were two playoff seasons, 1997-8 (Barnet 1 Colchester United 0, Colchester United 3 Barnet 1 - Agg 2-3) and 1999-2000 (Barnet 1 Peterborough United 2,Peterborough United 3 Barnet 0, Agg 1-5).

It was first round defeats against Woking in the FA Cup (1994-5 and 1995-6), Watford (1997-8), Hednesford Town (1998-9) and Burnley (1999-0) and a second round defeat against Wycombe (1996-7)  

2000s

Barnet's ten year reign in the football league came to an end in Season 2000-1 with the club returning to the Conference, losing 25 games in the process. A final day winner-takes-all match against Torquay United saw the Bees condemned with a 3-2 defeat.

The first season in the Conference was mixed. A strong start kept the Bees near the top with pacesetters Dagenham & Redbridge and Boston United, however a nightmare Christmas period saw the Bees slip dramatically out of the race. Manager John Still resigned in February and was succeeded by Peter Shreeves and Martin Allen. They guided the side to 5th after some excellent late season form. Also, the Bees reached the Southern Area Semi Final of the LDV Vans Trophy, eventually losing 2-0 to Cambridge United.

Optimism was high for the following season, however Barnet found themselves languishing around mid-table for the majority of the season, eventually finishing 11th. Peter Shreeves resigned in March and was succeeded as caretaker boss by Martin Allen, his assistant. The ongoing battle with Barnet Council was also at the forefront of the club, with plans for a new stadium at South Underhill being rejected, again threatening the existence of the club in Barnet.

The 2003/2004 season saw a huge overhaul in playing staff and the effect was immediate. The Bees were well in contention for the Play-Offs throughout the season and were threatening Chester City for the top spot. In March however, Martin Allen left for the Bees of Brentford, a month before the end of the season. Paul Fairclough took over on a temporary basis and guided the team into the Play-Offs on the last day at home to Leigh RMI. The Bees were paired against Shrewsbury Town and were beaten on penalties at Gay Meadow having drawn 2-2 on aggregate. It was a bitter pill to swallow, but Barnet were to come back bigger and stronger.

In 2004/2005, the Bees stormed the Conference, winning it by twelve points from Hereford United. Having gone top after a 1-0 win against Canvey Island in August, Barnet never looked back and stayed top for the rest of the season, destroying everything in their path. The first half of the season in particular was host to some scintillating performances as the goals flew in, home and away. The title was wrapped up with games and weeks to spare and supporters would be ready for life back in the Football League.

2005/2006 was a difficult return for the Bees. After a strong start, heading to the top of the league, the form soon slipped and Barnet toppled towards the bottom of the table. With the side struggling away from home in particular, it came down to the last day of the season at already relegated Rushden & Diamonds to be sure of survival. A 2-1 victory, the first away win since August saw that The Bees stayed up and finished 18th.

The season will surely be remembered by most Bees fans as the season they saw their side challenge the might of Manchester United at Old Trafford in the Carling Cup. After beating Bristol City and Plymouth Argyle, supporters could not believe their luck as Manchester United were pulled out of the hat. However, a red card for Ross Flitney after two minutes tarnished the evening, but the remaining ten battled heroically and a 4-1 defeat was a harsh reflection on the game.

Onto to 2006/2007 and a record FA Cup run. Before this season, Barnet had never passed the 3rd Round stage, but victories against Gainsborough Trinity and Northampton Town set up a home tie with Colchester United. After a postponement, the game took place the following midweek and a superb second half performance and a stunning winner by Jason Puncheon earnt the Bees a fourth round place. Barnet were drawn at home to Plymouth Argyle and optimism was high, however the Championship side were just too strong and ran out 2-0 winners. The Bees also enjoyed a trip to Leeds United in the Carling Cup.

Elsewhere in the League, a poor start was followed by an excellent run of form which propelled the team close to the Play-Offs. However, the form eventually dropped off towards the end of the season and Barnet ended up finishing in 14th place.