Farnborough were Southern League champions again in 1993–94, making an immediate return to the Conference. The club spent five seasons in the Conference until being relegated at the end of the 1998–99 season, which had seen them finish bottom of the table. They were placed in the Premier Division of the Isthmian League, which they went on to win in 2000–01, resulting in promotion back to the Conference. In 2002–03 the club progressed beyond the first round of the FA Cup for a second time; after a 5–1 win against Harrogate Town in the first round, they defeated Southport 3–0 in the second round and Third Division Darlington 3–2 in the third round. They were then drawn at home to Arsenal in the fourth round, although the game was switched to Highbury. Following a 5–1 defeat, manager Graham Westley left the club, also taking seven players with him as he moved to Stevenage Borough.