The 1998–99 FA Trophy was the thirtieth season of the FA Trophy.
The teams that given byes to this round are Cheltenham Town, Doncaster Rovers, Woking, Rushden & Diamonds, Morecambe, Hereford United, Hednesford Town, Northwich Victoria, Welling United, Yeovil Town, Hayes, Dover Athletic, Kettering Town, Stevenage Borough, Southport, Kidderminster Harriers, Farnborough Town, Leek Town, Telford United, Forest Green Rovers, Barrow, Kingstonian, Slough Town, Chorley, Colwyn Bay, Merthyr Tydfil, Leigh R M I, Sutton United, Hendon, Emley, Altrincham, Basingstoke Town, Atherstone United, St Albans City, Nuneaton Borough, Gravesend & Northfleet, Chesham United, Tamworth, Bromley, Rothwell Town, Dulwich Hamlet, Aylesbury United, Bromsgrove Rovers, Aldershot Town, Worksop Town, Sittingbourne, Ashford Town (Kent), Yeading, Alfreton Town, Hitchin Town, Oxford City, Fisher Athletic London, Margate, Droylsden, Lincoln United, Uxbridge, Raunds Town, Moor Green, Witton Albion, Romford, Clevedon Town, Bognor Regis Town, Havant & Waterlooville, Dartford, Worthing, Tonbridge Angels, Whitley Bay, Berkhamsted Town, Bedworth United, Racing Club Warwick, Shepshed Dynamo, Netherfield Kendal, Barton Rovers, Evesham United, Harrogate Town, Corby Town, Great Harwood Town, Andover, Burscough and Hucknall Town.