[2] The 1999–2000 Kent Football League Challenge Cup was won for the first time in their history by VCD Athletic.
[3] Deal Town reached the final but owing to fixture congestion from their extended run to the FA Vase Final they withdrew[4] (with Faversham Town, who they had defeated in their semi-final tie, taking their place).
The promotion of reserves teams into the Premier Division was not permitted.
There was a single League Cup competition for the teams in the section.
The competition for the 22 teams from the Reserves Section comprised a group phase (with four sections) with the group winners progressing to home and away aggregate semi-finals to produce the two finalists.