The 1999–2000 FA Trophy was the thirty-first season of the FA Trophy.
This season of the FA Trophy saw 177 teams participate, with matches starting in November 1999 and the final taking place in May 2000.
In the early rounds of the competition, lower ranked teams played each other, while higher ranked clubs entered the competition in the later stages. This edition was marked by exciting matches that showed the competitiveness of non-league clubs.
In the semifinals four teams fought for a place in the final, with matches being played over two legs, one at home and one away.
The 1999-2000 FA Trophy Final was held at the former Wembley Stadium in London on 14 May 2000. The competition finalists were Kingstonian and Kettering Town.
Kingstonian, the defending champions, emerged victorious once again, defeating Kettering Town 3-2 in a thrilling final.
1st round
Ties
Replays
2nd round
The teams that given byes to this round are Kingstonian, Scarborough, Kettering Town, Hayes, Rushden & Diamonds, Yeovil Town, Stevenage Borough, Northwich Victoria, Woking, Hednesford Town, Dover Athletic, Forest Green Rovers, Hereford United, Morecambe, Kidderminster Harriers, Doncaster Rovers, Telford United, Southport, Welling United, Nuneaton Borough, Altrincham, Sutton United, Farnborough Town, Tamworth, Bromley, Dulwich Hamlet, Aldershot Town, Worksop Town, Ashford Town (Kent), Droylsden, Uxbridge, Witton Albion, Dartford, Whitley Bay, Bedworth United, Barton Rovers, Evesham United, Harrogate Town, Worcester City, Bamber Bridge, Enfield, Gainsborough Trinity, Whitby Town, Crawley Town, Hyde United, Stalybridge Celtic, Weymouth, Winsford United, Billericay Town, Marine, Walton & Hersham, Lancaster City, Carshalton Athletic, Bishop Auckland, Canvey Island, Wealdstone, Folkestone Invicta, Newport I O W, Eastwood Town, Grays Athletic, Radcliffe Borough, Stafford Rangers, Bilston Town, Blakenall, Stocksbridge Park Steels, Sutton Coldfield Town, Gretna, Leyton Pennant, Witney Town, Wisbech Town, Erith & Belvedere, St Leonards, Whyteleafe, Stamford, Staines Town, V S Rugby, Yate Town, Workington and Bedford Town.