Slough Town had gained promotion to the Conference, the top level of non-league football, in 1990. The club struggled for a couple of seasons and briefly went into receivership in 1991. They finished an excellent fifth in 1993, but slumped and were relegated the following season. They were promoted straight back to the Conference the next year, despite finishing as runners-up to Enfield in the Isthmian League, because Enfield were unable to take their place in the top flight.

Slough Town's time in the Conference ended unhappily. After finishing 8th in 1998 they were expelled from the League because their ground did not meet the League's standards. The club was taken over by a consortium led by Martyn Deaner. They struggled at the lower level, and in 2001 were relegated from the Isthmian Premier League. Problems with the lease on Wexham Park meant that Slough Town had to move out in 2003, and have ground-shared with Windsor & Eton since.

However, things are looking up. 2004-5 was their best season for some time, as they won the Isthmian League Cup for the third time, and once again reached the 2nd round of the FA Cup, beating Walsall in round one.