El FA Trophy 1989-90 fue la vigésimo primera temporada del FA Trophy .
Los equipos que dieron pases directos a esta ronda son Telford United, Darlington, Kettering Town, Wycombe Wanderers, Boston United, Kidderminster Harriers, Barnet, Runcorn, Macclesfield Town, Yeovil Town, Northwich Victoria, Welling United, Cheltenham Town, Enfield, Sutton United, Altrincham, Fisher Athletic, Merthyr Tydfil, Barrow, Farnborough Town, Aylesbury United, Wealdstone, Dartford, Burton Albion, Hyde United, Wokingham Town, Newcastle Blue Star, Bishop Auckland, Redbridge Forest, Windsor y Eton, Billingham Synthonia y Tow Law Town.