Barnet were promoted back to the football league in 2005 and returned to playing in the League Cup, now renamed the Carling Cup. In the 1st Round they were drawn away at League One club,BristolCity and produced one of the shocks of the round with a 4-2 win which included a stunning individual goal from Nicky Bailey which was to later win the Goal of the Season award for 2005/06 at Barnet. Dwane Lee scored twice and Lee Roache scored the other goal in a splendid win for the Bees who at the time were top of League Two. The Barnet side that day was; Flitney, Hendon, King, Charles, Gross, Bailey, Bowditch (Norville), Lee, Graham, Strevens, Grazioli (Roache).
In the 2nd round, Barnet were drawn at home to Plymouth Argyle and gave another fine performance, winning 2-1 with goals from Simon King and Giuliano Grazioli to go through to the 3rd round of the League Cup for the first time in the club’s history. The draw for the 3rd round ensured that whatever the outcome, October 26th 2005 would be one of the highlights of Barnet’s history as the club was drawn away to play mighty Manchester United at Old Trafford.
On the day, the occasion started badly for the Bees. Travel problems meant that many fans had still not arrived when the game started and with only a few minutes gone, referee Richard Beeby made the decision that was to completely alter the course of the game for Barnet when he sent keeper, Ross Flitney off for handling the ball outside the penalty area. For poor Louis Soares, it meant that his day was ruined as he was the unlucky player to be substituted so that Scott Tynan could replace Flitney in goal. Manchester United scored from the free kick that followed the sending off and Barnet had another piece of bad luck when Giuliano Grazioli scored an equaliser only for the goal to be ruled out by Beeby when the goal appeared to be a perfectly good one. In the end, United won 4-1 but the Barnet fans sang throughout the game and did the players proud and they erupted when Dean Sinclair scored the only Barnet goal. The Barnet side that day was; Flitney, Hendon, Yakubu, King, Gross, Soares (Tynan), Sinclair, Bailey, Lee (Batt), Strevens, Grazioli (Hatch)
The following season, 2006/07, was the last season to date that Barnet have got past the first round. In the 1st round, they were drawn to play Cardiff City, as now in the Championship, at Ninian Park and were expected to loose. However, the Bees, with Joe Devera making his full debut for the club at right back, gave a superb performance and won comfortably 2-0 with both goals coming from Tresor Kandol, one in each half. The Barnet line up was; Flitney, Devera, Charles, Warhurst, Gross, Cogan, Sinclair, Bailey, Puncheon (Nicolau), Kandol, Vieira (Norville).
The 2nd round saw a trip to another Championship side, but this was a more glamorous tie as Barnet were drawn to play Leeds United at Elland Road. Barnet gave a good account of themselves and probably should have been awarded a penalty but in the end lost 3-1 with Magno Vieira scoring the Bees’ goal.
Since then, Barnet have failed to make it past the 1st round and in the next two seasons, they have been reduced to 10 men after having a player red carded. In 2007, they lost 5-2 at Norwich City after Neal Bishop was sent off and Norwich had gone 5-0 up by halt time. The Bees pulled back two goals in the second half through Jason Puncheon and Adam Birchall.
In 2008/09, Barnet went out at the same stage, losing 4-0 to Brighton and had Kenny Gillet sent off. The following season, 2009/10, the Bees gave a good account of themselves in the home tie with Watford but eventually went down 2-0 after extra time. In 2010/11, Barnet lost 3-0 away at Swansea City.
In 2011/12 the Bees won their first Carling Cup match for 5 years with a stunning 1-0 win at Championship club, Portsmouth. Mark Hughes scored the only goal of a game which the Bees dominated and could have won by more. Barnet were then unlucky to go out in the 2nd round at Burnley when, after going 2-0 down in the second half, the Bees fought back to 2-2 with goals from Ricky Holmes and substitute, Steve Kabba which pushed the tie into extra time. Unfortunately, Burnley grabbed a third to send the Bees out of the tournament but it had been a fine performance and the Bees’ best League Cup showing since 2006/07.
In 2012/13, Barnet were drawn away at another Championship club, this time Birmingham City but crashed out 5-1, Jon Nurse scoring the Barnet goal. At the end of the season, Barnet were relegated back to the Conference.