| 15/08/98 | Southampton | A | 2-1 | Riedle, Owen |
| 22/08/98 | Arsenal | H | 0-0 | |
| 29/08/98 | Newcastle United | A | 4-1 | Owen (3), Berger |
| 09/09/98 | Coventry City | H | 2-0 | Berger, Redknapp |
| 12/09/98 | West Ham United | A | 1-2 | Riedle |
| 15/09/98 | FC Kosice (UEFA Cup 1st Round 1st leg) | A | 3-0 | Berger, Riedle, Owen |
| 19/09/98 | Charlton Athletic | H | 3-3 | Fowler (2), Berger |
| 26/09/98 | Manchester United | A | 0-2 | |
| 29/09/98 | FC Kosice (UEFA Cup 1st Round 2nd leg) | H | 5-0 | Redknapp (2), Ince, Fowler (2) |
| 03/10/98 | Chelsea | H | 1-1 | Redknapp |
| 17/10/98 | Everton | A | 0-0 | |
| 20/10/98 | Valencia (UEFA Cup 2nd Round 1st leg) | H | 0-0 | |
| 24/10/98 | Nottingham Forest | H | 5-1 | Owen (4), McManaman |
| 27/10/98 | Fulham (Worthington Cup 3rd Round) | H | 3-1 | (og), Fowler, Ince |
| 31/10/98 | Leicester City | A | 0-1 | |
| 03/11/98 | Valencia (UEFA Cup 2nd Round 2nd leg) | A | 2-2 | McManaman, Berger |
| 07/11/98 | Derby County | H | 1-2 | Redknapp |
| 10/11/98 | Tottenham Hotspur (Worthington Cup 4th Round) | H | 1-3 | Owen |
| 14/11/98 | Leeds United | H | 1-3 | Fowler |
| 21/11/98 | Aston Villa | A | 4-2 | Ince, Fowler (3) |
| 24/11/98 | Celta Vigo (UEFA Cup 3rd Round 1st leg) | A | 1-3 | Owen |
| 28/11/98 | Blackburn Rovers | H | 2-0 | Ince, Owen |
| 05/12/98 | Tottenham Hotspur | A | 1-2 | Berger |
| 08/12/98 | Celta Vigo (UEFA Cup 3rd Round 2nd leg) | H | 0-1 | |
| 12/12/98 | Wimbledon | A | 0-1 | |
| 19/12/98 | Sheffield Wednesday | H | 2-0 | Berger, Owen |
| 26/12/98 | Middlesbrough | A | 3-1 | Carragher, Redknapp, Heggem |
| 28/12/98 | Newcastle United | H | 4-2 | Owen (2), Riedle (2) |
| 03/12/98 | Port Vale (FA Cup 3rd Round) | A | 3-0 | Owen, Ince, Fowler |
| 09/01/99 | Arsenal | A | 0-0 | |
| 16/01/99 | Southampton | H | 7-1 | Fowler (3), Matteo, Carragher, Owen, Thompson |
| 24/01/99 | Manchester United (FA Cup 4th Round) | A | 1-2 | Owen |
| 30/01/99 | Coventry City | A | 1-2 | McManaman |
| 06/02/99 | Middlesbrough | H | 3-1 | Owen, Heggem, Ince |
| 13/02/99 | Charlton Athletic | A | 0-1 | |
| 20/02/99 | West Ham United | H | 2-2 | Fowler, Owen |
| 27/02/99 | Chelsea | A | 1-2 | Owen |
| 13/03/99 | Derby County | A | 2-3 | Fowler (2) |
| 03/04/99 | Everton | H | 3-2 | Fowler (2), Berger |
| 05/04/99 | Nottingham Forest | A | 2-2 | Redknapp, Owen |
| 10/04/99 | Leeds United | A | 0-0 | |
| 17/04/99 | Aston Villa | H | 0-1 | |
| 21/04/99 | Leicester City | H | 0-1 | |
| 24/04/99 | Blackburn Rovers | A | 3-1 | McManaman, Redknapp, Leonhardsen |
| 01/05/99 | Tottenham Hotspur | H | 3-2 | Redknapp, Ince, McManaman |
| 05/05/99 | Manchester United | H | 2-2 | Redknapp, Ince |
| 08/05/99 | Sheffield Wednesday | A | 0-1 | |
| 16/05/99 | Wimbledon | H | 3-0 | Berger, Riedle, Ince |
