1998–99 Southend United F.C. season
The 1998–99 season saw Southend United compete in the Football League Third Division where they finished in 18th position with 54 points.
Final league table
Results
Southend United's score comes firstLegend
Football League Third Division
| Match | Date | Opponent | Venue | Result | Attendance | Scorers |
| 1 | 8 August 1998 | Scarborough | A | 2–1 | 2,298 | Coleman, Hails |
| 2 | 15 August 1998 | Shrewsbury Town | H | 2–1 | 3,734 | Clarke, Burns |
| 3 | 22 August 1998 | Peterborough United | A | 1–1 | 5,323 | Coleman |
| 4 | 29 August 1998 | Chester City | H | 0–1 | 4,421 | |
| 5 | 1 September 1998 | Carlisle United | A | 0–3 | 2,638 | |
| 6 | 5 September 1998 | Rotherham United | H | 3–0 | 3,479 | Newman, Fitzpatrick |
| 7 | 8 September 1998 | Halifax Town | H | 0–0 | 3,620 | |
| 8 | 12 September 1998 | Brighton & Hove Albion | A | 2–0 | 3,840 | Conlon, Whyte |
| 9 | 19 September 1998 | Cambridge United | H | 0–1 | 5,009 | |
| 10 | 26 September 1998 | Swansea City | A | 1–3 | 3,890 | Newman |
| 11 | 3 October 1998 | Rochdale | H | 1–1 | 3,686 | Maher |
| 12 | 10 October 1998 | Scunthorpe United | H | 1–1 | 3,686 | Maher |
| 13 | 17 October 1998 | Leyton Orient | H | 2–2 | 6,700 | Clarke, Fitzpatrick |
| 14 | 20 October 1998 | Mansfield Town | H | 1–2 | 3,250 | Whyte |
| 15 | 24 October 1998 | Hull City | A | 1–1 | 3,551 | Conlon |
| 16 | 31 October 1998 | Darlington | H | 2–1 | 3,527 | Maher, Newman |
| 17 | 7 November 1998 | Exeter City | A | 1–2 | 3,085 | Burns |
| 18 | 10 November 1998 | Brentford | A | 1–4 | 4,285 | Burns |
| 19 | 21 November 1998 | Plymouth Argyle | H | 1–0 | 3,814 | Newman |
| 20 | 28 November 1998 | Cardiff City | A | 0–2 | 4,638 | |
| 21 | 12 December 1998 | Barnet | H | 2–3 | 4,311 | Coleman, Burns |
| 22 | 19 December 1998 | Hartlepool United | A | 4–2 | 1,889 | Houghton, Newman, Fitzpatrick, Conlon |
| 23 | 26 December 1998 | Peterborough United | H | 2–0 | 6,159 | Newman, Fitzpatrick |
| 24 | 28 December 1998 | Torquay United | A | 0–2 | 3,228 | |
| 25 | 2 January 1999 | Chester City | A | 1–1 | 2,574 | Newman |
| 26 | 9 January 1999 | Scarborough | H | 1–0 | 3,453 | Livett |
| 27 | 16 January 1999 | Shrewsbury Town | A | 1–3 | 2,132 | Maher |
| 28 | 23 January 1999 | Carlisle United | H | 0–1 | 4,120 | |
| 29 | 30 January 1999 | Torquay United | H | 0–0 | 3,567 | |
| 30 | 6 February 1999 | Rotherham United | A | 2–2 | 3,895 | Rapley |
| 31 | 13 February 1999 | Halifax Town | A | 1–3 | 2,302 | Rapley |
| 32 | 20 February 1999 | Brighton & Hove Albion | H | 3–0 | 6,066 | Rapley, Barry Hunter |
| 33 | 27 February 1999 | Cambridge United | A | 0–3 | 5,013 | |
| 34 | 6 March 1999 | Swansea City | H | 2–0 | 3,713 | Conlon, Roach |
| 35 | 13 March 1999 | Exeter City | H | 0–0 | 3,695 | |
| 36 | 20 March 1999 | Darlington | A | 1–2 | 2,516 | Conlon |
| 37 | 26 March 1999 | Hull City | H | 0–1 | 4,149 | |
| 38 | 30 March 1999 | Rochdale | A | 0–1 | 1,334 | |
| 39 | 3 April 1999 | Leyton Orient | A | 3–0 | 6,515 | Campbell, Coleman |
| 40 | 5 April 1999 | Scunthorpe United | H | 0–1 | 4,814 | |
| 41 | 10 April 1999 | Mansfield Town | A | 0–0 | 2,624 | |
| 42 | 13 April 1999 | Cardiff City | H | 0–1 | 4,076 | |
| 43 | 17 April 1999 | Plymouth Argyle | A | 3–0 | 3,949 | Conlon, Houghton |
| 44 | 24 April 1999 | Brentford | H | 1–4 | 5,428 | Clarke |
| 45 | 1 May 1999 | Barnet | A | 2–0 | 2,704 | Houghton, Hodges |
| 46 | 8 May 1999 | Hartlepool United | H | 1–1 | 4,865 | Maher |
FA Cup
| Round | Date | Opponent | Venue | Result | Attendance | Scorers |
| R1 | 14 November 1998 | Doncaster Rovers | H | 0–1 | 3,740 |
League Cup
| Round | Date | Opponent | Venue | Result | Attendance | Scorers |
| R1 1st Leg | 11 August 1998 | Gillingham | H | 1–0 | 2,509 | Newman |
| R1 2nd Leg | 18 August 1998 | Gillingham | A | 1–0 | 3,417 | Clarke |
| R2 1st Leg | 16 September 1998 | Coventry City | A | 0–1 | 6,631 | |
| R2 2nd Leg | 22 September 1998 | Coventry City | H | 0–4 | 6,292 |
Football League Trophy
| Round | Date | Opponent | Venue | Result | Attendance | Scorers |
| R1 | 5 January 1999 | Exeter City | A | 1–3 | 1,143 | Maher |