Although United were relegated in 1998, they bounced straight back the following season under manager Andy Sinnott, who also led them to the semi-finals of the FA Vase and to within two points of achieving promotion to the Premier Division.

In October 2003 the club reached the fourth qualifying round of the FA Cup for the first time in their history, going down 2–1 to Conference side Farnborough Town.

In 2005 severe financial difficulties hit the club, with bailiffs seizing assets to offset unpaid VAT bills, and the landlord of their Windmill Road stadium serving them with notice of eviction.

The club managed to limp to the end of the season playing at the ground of neighbours Aylesbury United and a rock-bottom finish saw them relegated back to the Hellenic League after 18 years away.

During the summer of 2006, Aylesbury were also evicted from their ground, leaving Thame homeless once again, leading to a new groundshare arrangement with AFC Wallingford.

In October 2007 it was announced that the club planned to move to a multi-million pound venue at Church Farm in the North of Thame.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.