Following, Barnet’s relegation to the Conference in 2001, the Bees were still eligible for the LDV Trophy in 2001/02. The Bees enjoyed their best ever run in this tournament reaching the semi-finals of the Southern Section before going out to Division 2 side, Cambridge United 2-0 at the Abbey Stadium.
On the way to the Semi-Final, Barnet defeated three league sides. In the 1st round they overcame Bournemouth 2-1 at Underhill with goals from Robbie Sawyers and Roy Essendoh. The next round saw a trip to Northampton and a Lee Flynn goal was enough for the Bees to go through to the 3rd round on the back of a 1-0 win. In the 3rd round, Barnet produced a tremendous performance in defeating Reading 4-1 at Underhill thanks to two goals from Ben Strevens and one apiece for Greg Heald and Austin Berkley.
In 2002/03, the club were refused entry to the LDV Vans trophy to due Football League ground regulations that Barnet fell foul of. However, changes in the regulations meant that Barnet, having finished in the top half of the Conference in 2003, returned to the LDV Trophy in 2003/04. Unfortunately, the Bees went out of the trophy in the 1st round, losing on penalties to Brentford after having held the Division 2 club to 3-3 after extra time. A young Barnet side had at one point been 2-0 up, but had a goal from Liam Hatch to thank for taking the game to extra time. Barnet’s other goals were scored by Solomon Henry and Guy Lopez, whose goal, a stunning strike from more than 20 yards, was eventually named Barnet Supporters’ Club Goal of the Season. The Barnet side that day was; Gore; Rooney, Cumberbatch, King, Taggart; Lopez, Henry (Freeman), Bai Mass, Hogg; Sylla (Hatch), Roache.
In 2004/05, Barnet defeated local rivals, Stevenage Borough in the 1st round with 2 goals from Nicky Bailey and one from Lee Roache, but went out in the 2nd round losing 2-0 at Bristol Rovers. At the end of the season, Barnet were Conference Champions and were promoted to League Two and, meanwhile, the structure of the LDV Vans trophy changed with it becoming solely for League 1 and 2 clubs as Conference clubs were not eligible any more for the tournament.
In 2005/06, Barnet defeated League One side, BristolCity3-2 at Underhill in the 1st round with goals from Dean Sinclair, Ben Strevens and Jason Norville, but then lost 3-0 to MK Dons in the 2nd round.
For the following season, 2006/07, the Football League Trophy had new sponsors and a new name; the Johnstone’s Paint Trophy and the Bees won their first JPT match 1-0 at NottsCounty; Tresor Kandol scoring the only goal. However, in the 2nd round, two Kandol goals were not enough for the Bees asCheltenham won 3-2.
The next two seasons saw Barnet go out in the 1st round. In 2007/08, the Bees lost 2-1 atBrighton; Adam Birchall scoring for Barnet and in 2008/09, in the middle of a dreadful start to the league season, Barnet lost 4-2 at Dagenham & Redbridge, Birchall scoring both Barnet goals.
A bright start to the 2009/10 league season under Ian Hendon saw Barnet beat high flying League One side, Millwall, 2-0 at Underhill with Jake Hyde and Ismail Yakubu scoring for the Bees but a trip to Charlton Athletic in the 2nd round saw Barnet go out 4-1 after John O’Flynn had put Barnet ahead early on.
Last season, following another poor start to the league season under Mark Stimson, Barnet, after having received a bye in the 1st round, went down 3-1 at home to Southend United at Underhill following a lamentable performance by the Bees, Mauro Vilhete scoring for Barnet.
However, this season the Bees achieved one of their best results in this tournament by overcoming League One, Colchester United, 3-1 way from home; Ricky Holmes, Izale McLeod and Steve Kabba grabbing the Barnet goals under new boss Lawrie Sanchez.