In 1991, Barnet won the Conference and were promoted to the football league for the first time in their history. In 1991/92, they retained the Herts Senior Cup by beating Hemel Hempstead Town in the final 4-1; Gary Poole, Roger Willis, Frank Murphy and Mark Carter scoring the goals in a match played at Clarence Park, St. Albans. The Bees beat Stevenage Borough (6-0) and Borehamwood (3-0) on the way to the final.
The next season, Barnet were promoted to the 2nd division (now League One) of the football league and they made it a hat trick of wins in the Herts Senior Cup beating Watford 4-1 in the final at Bishops Stortford after wins over Stevenage Borough (3-1) and St Albans City (2-1) in the previous rounds. Barnet goals in the final came from Mick Bodley, Gary Bull, Jonathon Hunt and Darren Oxbrow.
In the following two seasons, the Bees went out at the first attempt, both times to Watford and by the same score each time; 0-3. But in 1996, the Bees regained the trophy, beating Watford 2-1 at Clarence Park with Paul Wilson and Terry Robbins scoring for the Bees. St. Albans City (3-0), Borehamwood (3-2) and Hitchin Town (1-0) were defeated on the way to the final.
The following season, Barnet lost 2-1 in the semi final to Borehamwood after defeating Watford 2-0 in the 3rd round. In 1997/98, Barnet again reached the semi final after wins over Cheshunt (4-2), Hertford Town (2-0) and St Albans (3-0). In the semi final at home to Watford, Barnet’s John Doolan was sent off in a match that the Bees lost 2-1. Doolan, subsequently received a three match ban and Barnet manager, John still refused to enter the club for the following two seasons in protest.
Barnet re-entered the tournament for the 2000/01 season, the year the club was relegated back to the Conference. Barnet only reached the 3rd round before losing 3-0 to Baldock Town having beaten Bishops Stortford (6-1) and Borehamwood (4-3) in the opening two rounds. In the following two seasons, Barnet went out at the first attempt, losing 2-0 at home to Watford in 2001/02 and 2-0 away at Potters Bar Town the following year.
In 2003/04, Barnet lost 3-2 after extra time in the semi final at Borehamwood, after disposing of Ware (4-1) and Cheshunt (4-1). In the game against Ware, played at Underhill, Bees’ ‘super fan’, Steve Percy cam on as a substitute, much to the annoyance of the Ware side and was involved in one of the Ware players being sent off!!
The following two seasons saw Barnet go out at the first attempt, to Tring Athletic (on penalties after drawing 1-1) and Oxhey Jets (1-2) respectively.
It had been 14 years since the club had won the County Cup, but in 2007, Barnet took the trophy back to Underhill after beating Hemel Hempstead Town, 4-2 at the County Ground in Letchworth, Liam Hatch scoring twice and Joe Devera and Giuliano Grazioli grabbing one apiece. Welwyn Garden City (4-0 after a replayed 2nd round match), Hertford Town (1-0) and Bishops Stortford (2-0) were defeated on the way to the final.
In 2007/08, Barnet started their defence of the trophy with a fine 4-2 away win at Stevenage Borough in the 2nd round, but have failed to win a game in the tournament since then. The Bees lost 4-1 away at Ware in the 3rd round and 3-0 at St. Albans City, the following season. Last season, the Bees again went out at the first attempt, this time losing 5-3 away at Hemel Hempstead Town.
The following season, Barnet went out in the 1st round losing 3-0 at St Albans City and the Bees went out at the first time of asking in 2009/10 losing 5-3 at Hemel Hempstead Town.
In 2010/11, the Bees had a bye into the 2nd round agin and they defeated Hadley 4-1 in the 2nd round with goals from Scott, Mauro Vilhete, Charlie Stimson and an own goal. In the 3rd round, the Bees won 6-2 at Broxbourne Borough with goals from Adjeman-Pamboe, Scott, Lockhart-Adams, Vilhete and two from Charlie Stimson.
Mauro Vilhete scored the only goal in the semi final at Cheshunt and so the Bees were in the County Cup final for the first time since they won it in 2007. In the final, the Bees met Stevenage and won the tournament with a 2-1 victory, Charlie Stimson scoring both goals.
Last season, the Bees beat Hemel Hempstead Town 2-1 after extra time in the 2nd round with goals from Jordan Parkes and Jamal Lowe, but lost 5-0 at Stevenage in the 3rd round.