The 1988–89 FA Trophy was the twentieth season of the FA Trophy.
First qualifying round
Ties
Replays
2nd replay
Second qualifying round
Ties
Replays
2nd replay
Third qualifying round
Ties
Replays
2nd replay
1st round
The teams that given byes to this round are Enfield, Newport County, Barnet, Kettering Town, Runcorn Linnets, Telford United, Stafford Rangers, Kidderminster Harriers, Sutton United, Maidstone United, Weymouth, Macclesfield Town, Cheltenham Town, Altrincham, Fisher Athletic, Boston United, Aylesbury United, Chorley, Yeovil Town, Bath City, Wealdstone, Dartford, Marine, Bromsgrove Rovers, Burton Albion, Fareham Town, Blyth Spartans, Hyde United, Barrow, Bromley, Wokingham Town and Newcastle Blue Star.