The 1998–99 FA Cup qualifying rounds opened the 118th season of competition in England for 'The Football Association Challenge Cup' (FA Cup), the world's oldest association football single knockout competition. A total of 558 clubs were accepted for the competition, down five from the previous season's 563.
The large number of clubs entering the tournament meant that the competition started with preliminary and four qualifying knockouts for these non-League teams. The 32 winning teams from fourth round qualifying progressed to the First round proper, where League teams tiered at Levels 3 and 4 entered the competition.
Matches were played on weekend of Saturday 21 August 1998. A total of 172 clubs took part in this stage of the competition, including 44 clubs from the four divisions at Level 7 of English football and 128 clubs from sixteen lower-level leagues, while other 44 clubs from the four divisions at Level 7 of English football and 162 clubs from lower-level leagues get a bye to the first round qualifying.
Matches were played on weekend of 4 September 1998. A total of 292 clubs took part in this stage of the competition, including the 86 winners from the preliminary round and 206 clubs, who get a bye to this round, including 44 clubs from the four divisions at Level 7 of English football.
Matches were played on weekend of 18 September 1998. A total of 212 clubs took part in this stage of the competition, including the 146 winners from the first round qualifying and 66 Level 6 clubs, from Premier divisions of the Isthmian League, Northern Premier League and Southern Football League, entering at this stage.
Matches were played on weekend of 2 October 1998. A total of 128 clubs took part, 106 having progressed from the second round qualifying and 22 clubs from Football Conference, forming Level 5 of English football, entering at this stage.
