After being relegated from the Football League in 2001, Barnet resumed playing in the FA Trophy for the 2001/02 season. They began their campaign with a trip to Fisher Athletic and won 5-0 with two goals for Wayne Purser and one apiece for Leon Bell, Greg Heald & Mark Gower. However, in the 4th round, Gower missed a golden opportunity to win the home tie with Scarborough but missed a penalty in time added on. Ben Strevens and Purser scored in the replay which ended in a 2-2 draw but, ironically, Scarborough won on penalties.
In 2002/03, Barnet lost in the 3rd round at Forest Green with Purser and Neil Midgley scoring in a 4-2 defeat. The following season, Barnet knocked out Dover at Underhill in the 3rd round winning 3-2 with two goals from Geoff Pitcher and one from Lee Roache but Barnet were kicked out of the competition for playing an ineligible player, Adam Campion, as a substitute.
In 2004/05, Nicky Bailey scored the only goal to give Barnet a 1-0 home win over Farnborough Town in the 3rd round and scored again in the 4th round away at Carlisle but Barnet, playing a weakened line up, lost 4-1. At the end of the season, Barnet were Conference champions and were promoted to League Two.
In 2013, Barnet were relegated again back to the Conference. Last season, the Bees won 1-0 away at Hayes & Yeading in the 1st round with the goal coming from George Sykes. However, in the 2nd round, a Keanu Marsh-Brown goal was not enough to stop Grimsby winning 2-1 at the Hive.
This season, a very young Barnet side drew 0-0 away at Concord Rangers in the 1st round.