El FA Trophy 1998-99 fue la trigésima temporada del FA Trophy .
Los equipos que pasaron directamente a esta ronda son 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 RMI, 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, Ciudad de Alfreton, Ciudad de Hitchin, Ciudad de Oxford, Fisher Athletic London, Margate, Droylsden, Lincoln United, Uxbridge, Ciudad de Raunds, Moor Green, Witton Albion, Romford, Ciudad de Clevedon, Ciudad de Bognor Regis, Havant y Waterlooville, Dartford, Worthing, Tonbridge Angels, Whitley Bay, Ciudad de Berkhamsted, Bedworth United, Racing Club Warwick, Shepshed Dynamo, Netherfield Kendal, Barton Rovers, Evesham United, Ciudad de Harrogate, Ciudad de Corby, Ciudad de Great Harwood, Andover, Burscough y Ciudad de Hucknall.