The 1978–79 FA Trophy was the tenth season of the FA Trophy, and this was to be the last season in which the Northern Premier League, Southern League and Isthmian League would be Level 5 in the English Pyramid System.
Preliminary round
Ties
Replays
2nd replay
First qualifying round
Ties
Replays
2nd replays
3rd replay
Second qualifying round
Ties
Replays
Third qualifying round
Ties
Replays
2nd replay
1st round
The teams that given byes to this round are Altrincham, Southport, Scarborough, Matlock Town, Morecambe, Stafford Rangers, Weymouth, Bedford Town, Kettering Town, Boston United, Atherstone Town, Runcorn, Lancaster City, Enfield, Wycombe Wanderers, Dagenham, Tooting & Mitcham United, Leatherhead, Spennymoor United, Falmouth Town, Nuneaton Borough, Bangor City, Hendon, Slough Town, Winsford United, Crook Town, Bath City, Maidstone United, Worcester City, Marine, Blyth Spartans and Whitby Town.