| Saturday 15th August 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 1-2 | Nantwich Town | |
| Tuesday 18th August 1998 | Premier Division | ||
|---|---|---|---|
| Maine Road | 0-3 | Bootle | |
| Saturday 22nd August 1998 | Premier Division | ||
|---|---|---|---|
| Rossendale United | 1-0 | Bootle | |
| Tuesday 25th August 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 0-3 | Kidsgrove Athletic | |
| Saturday 29th August 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 0-1 | Leek CSOB | |
| Thursday 3rd September 1998 | Premier Division | ||
|---|---|---|---|
| Skelmersdale United | 5-1 | Bootle | |
| Saturday 5th September 1998 | Premier Division | ||
|---|---|---|---|
| Mossley | 5-0 | Bootle | |
| Tuesday 8th September 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 0-6 | Mossley | |
| Tuesday 15th September 1998 | Premier Division | ||
|---|---|---|---|
| Vauxhall GM | 1-1 | Bootle | |
| Saturday 19th September 1998 | F.A. Challenge Cup 1st Qualifying Round | ||
|---|---|---|---|
| Bootle | 2-3 | Bradford Park Avenue | |
| Wednesday 23rd September 1998 | Premier Division | ||
|---|---|---|---|
| St Helens Town | 3-0 | Bootle | |
| Saturday 26th September 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 2-3 | Atherton Collieries | |
| Tuesday 29th September 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 1-2 | Cheadle Town | |
| Saturday 3rd October 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 4-2 | Skelmersdale United | |
| Saturday 10th October 1998 | F.A. Carlsberg Vase 2nd Qualifying Round | ||
|---|---|---|---|
| Crook Town | 2-3 | Bootle | |
| Saturday 17th October 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 1-2 | Clitheroe | |
| Saturday 7th November 1998 | F.A. Carlsberg Vase 1st Round | ||
|---|---|---|---|
| West Auckland Town | 1-0 | Bootle | |
| Tuesday 10th November 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 0-4 | St Helens Town | |
| Saturday 14th November 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 0-1 | Maine Road | |
| Saturday 21st November 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 0-2 | Workington | |
| Saturday 28th November 1998 | Premier Division | ||
|---|---|---|---|
| Newcastle Town | 4-0 | Bootle | |
| Saturday 5th December 1998 | Premier Division | ||
|---|---|---|---|
| Holker Old Boys | 1-1 | Bootle | |
| Saturday 12th December 1998 | Premier Division | ||
|---|---|---|---|
| Bootle | 1-2 | Ramsbottom United | |
| Saturday 19th December 1998 | Premier Division | ||
|---|---|---|---|
| Clitheroe | 6-0 | Bootle | |
| Saturday 2nd January 1999 | Premier Division | ||
|---|---|---|---|
| Workington | 4-0 | Bootle | |
| Saturday 9th January 1999 | Premier Division | ||
|---|---|---|---|
| Atherton Collieries | 2-0 | Bootle | |
| Saturday 16th January 1999 | Premier Division | ||
|---|---|---|---|
| Bootle | 1-3 | Rossendale United | |
| Tuesday 19th January 1999 | Premier Division | ||
|---|---|---|---|
| Salford City | 3-1 | Bootle | |
| Saturday 23rd January 1999 | Premier Division | ||
|---|---|---|---|
| Bootle | 1-0 | Holker Old Boys | |
| Saturday 30th January 1999 | Premier Division | ||
|---|---|---|---|
| Nantwich Town | 0-0 | Bootle | |
| Saturday 6th February 1999 | Premier Division | ||
|---|---|---|---|
| Glossop North End | 1-2 | Bootle | |
| Saturday 13th February 1999 | Premier Division | ||
|---|---|---|---|
| Bootle | 3-1 | Glossop North End | |
| Saturday 20th February 1999 | Premier Division | ||
|---|---|---|---|
| Atherton LR | 1-5 | Bootle | |
| Tuesday 23rd February 1999 | Premier Division | ||
|---|---|---|---|
| Prescot Cables | 2-2 | Bootle | |
| Saturday 27th February 1999 | Premier Division | ||
|---|---|---|---|
| Ramsbottom United | 1-2 | Bootle | |
| Saturday 13th March 1999 | Premier Division | ||
|---|---|---|---|
| Cheadle Town | 2-3 | Bootle | |
| Friday 26th March 1999 | Premier Division | ||
|---|---|---|---|
| Kidsgrove Athletic | 0-2 | Bootle | |
| Monday 5th April 1999 | Premier Division | ||
|---|---|---|---|
| Bootle | 1-2 | Prescot Cables | |
| Saturday 10th April 1999 | Premier Division | ||
|---|---|---|---|
| Bootle | 0-2 | Vauxhall GM | |
| Saturday 17th April 1999 | Premier Division | ||
|---|---|---|---|
| Leek CSOB | 0-0 | Bootle | |
| Saturday 24th April 1999 | Premier Division | ||
|---|---|---|---|
| Bootle | 0-0 | Atherton LR | |
| Tuesday 27th April 1999 | Premier Division | ||
|---|---|---|---|
| Bootle | 1-1 | Newcastle Town | |
| Saturday 1st May 1999 | Premier Division | ||
|---|---|---|---|
| Bootle | 1-3 | Salford City | |
