Back in the Conference after 10 years in the football league, Barnet returned to the FA trophy with a comfortable 5-0 win at Fisher Athletic in the 3rd round. Two goals from Wayne Purser and a goal apiece from Greg Heald, Mark Gower and Leon Bell saw them through to the 4th round where they met Scarborough at Underhill. The Barnet side that day was, Naisbitt, Gledhill, Sawyers, Bell, Heald, Arber, Berkley (Taylor), Niven, Purser, Strevens (Midgley), Gower.
The Bees had the perfect chance of going through to the 5th round when they were awarded a penalty right at the end of a match that was, up to then, goalless. Mark Gower was entrusted with the penalty but he missed and Scarborough won the replay 5-3 0n penalties, ironically, after the match had ended 2-2 with Purser and Ben Strevens scoring for Barnet.
Barnet have never had such a good chance of progressing to the later stages of the FA Trophy since. In 2002/03 they went out at the first time of asking, losing 4-2 at Forest Green Rovers, Purser and Neil Midgley scoring for Barnet. The following season, 2003/04, they beat Dover Athletic 3-2 at home in the 3rd round with two goals from Geoff Pitcher and one from Lee Roache but were then expelled from the competition as they had played an illegible player, Adam Campion, who had already played in the competition that season for Aylesbury.
In 2004/05, Barnet did at least get past the 3rd round when they defeated Farnborough 1-0 at home with Nicky Bailey scoring the only goal of the match. The Barnet side was; Gore, Hendon, Champion, King, Clist, Lopez (Elmes), Batt, Bailey, Strevens, Hatch, McBean (Grazioli). However, in the 4th round they lost 4-1 to Carlisle United, Nicky Bailey scoring the Barnet goal which turned out to be the last Barnet goal in the FA Trophy as the Bees ended the season as Nationwide Conference champions and were promoted to League Two.
After being relegated back to the Conference in 2013, Barnet made their first appearance in the FA Trophy for nearly 9 years, winning 1-0 away at Hayes & Yeading in the 1st round of the competition. George Sykes scored a late winner for the Bees.