They again reached the FA Cup third round in the 2001–02 season, losing 4–1 to Ipswich Town after taking the lead, and finished second in the Conference, missing promotion to the Football League on goal difference.
The following season saw another run in the FA Cup, beating Plymouth Argyle after a replay in the Third Round before losing 1–0 to Norwich City thanks to an injury time goal.
Their league form was not particularly good until the latter stages of the season when they won eleven consecutive games and qualified for the play-off final, losing 3–2 in extra-time to Doncaster Rovers.
In May 2004 he took over as manager of ambitious Isthmian League side Hornchurch, but left shortly after the club went into administration in January 2005 after their owners, the Carthium Group ceased trading.
[10] Following his sacking at Ebbsfleet, Hill was set to take over at National League South club Chelmsford City in February 2020, before the deal fell through during contract negotiations.