The quick reformation meant that the new Dover club retained the last club's Southern league Southern division position.
Manager Chris Kinnear guided Athletic to the Conference, before, after a bad start to the 1994/95 season was fired. After a succession of unsuccessful managers, Dover found Bill Williams. Williams kept them in the Conference, took them to the F.A. Trophy Semis' in 1998 and made sure they completed their best Conference campaign so far, finishing sixth in season 1999/2000.
In November 2000 a new era in the clubs history began. John Husk stepped down as chairman to make way for Jim Gleeson to take over. With new money available, Whites were looking to consolidate on last seasons impressive finish, however they ended a disappointing campaign in 15th position. There was more bad news in May when Bill Williams resigned as manager.