Barnet were now back in the Conference following relegation from the Football League in 2001. However, at the time, the Football League Trophy (sponsored by LDV Vans) included Conference clubs as well as clubs from the bottom two tiers of the Football League and so Barnet continued to play in this tournament and, in 2001/02, they had their best run so far reaching the Southern area Semi Final before losing 2-0 at Cambridge United, then a Division 2 club.
The Bees reached the semi final by beating first Bournemouth in the 1st round, 2-1 at Underhill with goals from Robbie Sawyers and Roy Essendoh; Northampton away, 1-0 in the 2nd round through a goal by Lee Flynn and Reading 4-1 at Underhill with two goals from Ben Strevens and one apiece for Greg Heald and Austin Berkeley.
The following season, Barnet were barred from the competition due to problems about the ground capacity at Underhill as the Football League’s requirements at the time stated that clubs should be able to hold 6,ooo fans, which would have precluded any chance of the Bees gaining promotion and also lost them their place in the FLT.
However, by the following season, all this had changed again with the ground capacity requirement reduced to 5,000 and in 2003/04, Barnet resumed their place in the tournament. They went out in the first round, following an exciting 3-3 draw at Underhill against Brentford, playing with a very young side who had been 2-0 up at half time against the Division 2 side. The ’other Bees’ eventually won through on penalties. Barnet’s goals came from Solomon Henry, Liam Hatch and Guy Lopez, whose goal, his only goal for the club, was later voted goal of the season at Barnet.
In 2004/05, Barnet reached the 2nd round, beating local rivals, Stevenage Borough in the 1st round, 3-1 after extra time with Nicky Bailey scoring twice and Lee Roache scoring the other goal. In the 2nd round, an under strength Barnet side lost 2-0 at Bristol Rovers. At the end of the season, Barnet wer promoted back to the Football League as Conference champions.
Since returning to the Football League, Barnet’s performances in the FLT have mostly been less than outstanding though they started well enough, defeating League One club, Bristol City 3-2 in the 1st round of the LDV Trophy in 2005/06 with goals from Jason Norville, Dean Sinclair and Ben Strevens. However, they went out in the 2nd round losing 3-0 to MK Dons at Underhill.
By this time, the FLT was only for clubs from the bottom two tiers of the Football League, the Conference clubs being excluded from 2005. The next season, 2006/07, saw new sponsors, Johnstone’s Paints. Barnet reached the 2nd round again, defeating Notts County away, 1-0 through a Tresor Kandol goal in the 1st round but losing a tight 2nd round match, 3-2 at Cheltenham with Kandol scoring both Barnet goals.
The following two seasons saw Barnet go out at the first attempt; losing 2-1 at Brighton in 2007/08, Adam Birchall scoring for the Bees and 4-2 at Dagenham & Redbridge in 2008/09; Birchall scoring twice.
In 2009/10, Barnet defeated Millwall, then a League One side, comfortably by 2-0 at Underhill with goals from Jake Hyde and Ismail Yakubu before going out to another League One side, Charlton Athletic in the second round; the Bees losing 4-1 at the Valley, John O’Flynn scoring the Barnet goal. In 2010/11, Barnet went out very tamely to Southend United, 3-1 at Underhill at the first attempt with sub, Mauro Vilhete scoring for the Bees.
Last season, 2011/12, saw Barnet’s best ever season in this competition. The Bees defeated League One, Colchester United in the 1st round, 3-1 away with goals from Steve Kabba, Ricky Holmes and Izale McLeod. In round 2, Barnet were again drawn away, this time to Gillingham and they won again by 3-1, McLeod scoring twice and Mark Marshall the other.
In the quarter finals, Barnet were again away, at Cheltenham Town and came away 2-0 winners, Marshall and Charlie Taylor scoring. Finally, in the semi final, Barnet were drawn at home against League One, Brentford. The match ended goalless and went to extra time and penalties, which Barnet won 5-3. Keeper, Dean Brill was the Barnet hero that night.
So Barnet reached the Southern Area Final and were just two legs away from a March date at Wembley. Sadly it wasn’t to be as Swindon Town won 2-1on aggregate. The first match at Underhill ended in a 1-1 draw; Mark Hughes scoring for the Bees, while in the return leg, Barnet never really got going, had Charlie Taylor sent off and lost 1-0. So the Wembley dream died for another season. Even so, it was definitely Barnet’s best ever performance in this competition.
In 2012/13, Barnet travelled to meet Leyton Orient in a second round tie having received a bye in the 1st round. Orient won 1-0.