The 2003–04 Kent Football League Challenge Cup was won by Thamesmead Town.
The newly formed single Division One featured twelve clubs, the six highest ranked teams from each of the previous seasons Division One North (Cray Wanderers R, Thamesmead Town R, Danson Furness, Corinthian, Erith Town R and Dartford R) and Division One South (Deal Town R, Herne Bay R, Dover Athletic R, Ashford Town (Kent) R, Ramsgate R and Hastings United R).
At the end of the season champions Corinthian and runners-up Dover Athletic R resigned from the league – the former were the only non-reserves team to have won a division in the Reserves Section.
The newly formed Division Two featured thirteen clubs, the six lowest ranked teams from the previous seasons Division One North (Chatham Town R, Beckenham Town R, Tunbridge Wells R, Lordswood R, VCD Athletic R and Erith & Belvedere R) and five (following the withdrawal of Margate R) from Division One South (Sittingbourne R, Folkestone Invicta R, Maidstone United R, Whitstable Town R and Hythe Town R) together with two additional clubs: At the end of the season Erith & Belvedere R and Maidstone United R were promoted to Division One and Groundhoppers left the League after one season.
The 2003–04 Kent Football League Reserves Cup was won by Cray Wanderers R. The competition was contested by all 25 teams of the Reserves Section over a total of five rounds: the first three were single match knock-out rounds, followed by the semi-finals on an aggregate basis (home and away matches) and then the final match played on a neutral ground (at Chatham Town F.C.