| Season: | 1998–99 |
| Mgrtitle: | Manager |
| Chairman: | Frank Teasdale |
| Chrtitle: | Chairman |
| League Result: | 15th |
| Cup1 Result: | 1st Round |
| Cup2 Result: | 1st Round |
| Cup3 Result: | 1st Round |
| League Topscorer: | Andy Payton (20) |
| Season Topscorer: | Andy Payton (23) |
| Highest Attendance: | 17,251 v Manchester City (9 March 1999) |
| Lowest Attendance: | 5,453 v Bury (18 August 1998) |
| Average Attendance: | 10,109[1] |
| Pattern B1: | _vneck |
| Pattern So1: | _band_blue |
| Leftarm1: | 3BB9FF |
| Body1: | 990033 |
| Rightarm1: | 3BB9FF |
| Shorts1: | 990033 |
| Socks1: | 3BB9FF |
The 1998–99 season was Burnley's 4th successive season in the third tier of English football. They were managed by Stan Ternent in his first full season since he replaced Chris Waddle at the beginning of the campaign.
|}
| Pos | Player | From | Fee | Date | |
|---|---|---|---|---|---|
| FW | Free | 1 July 1998 | |||
| GK | Loan | 7 August 1998 | |||
| GK | Loan | 12 August 1998 | |||
| GK | Loan | 15 August 1998 | |||
| DF | £40k | 28 August 1998 | |||
| DF | Free | 28 August 1998 | |||
| DF | Loan | 23 October 1998 | |||
| GK | £100k | 18 November 1998 | |||
| MF | Loan | 26 November 1998 | |||
| DF | Free | 17 December 1998 | |||
| DF | £750k | 30 December 1998 | |||
| FW | Free | 1 January 1999 | |||
| MF | £350k | 8 January 1999 | |||
| MF | £225k | 12 February 1999 | |||
| MF | Loan | 12 March 1999 | |||
| DF | Loan | 12 March 1999 | |||
| DF | £20k | 16 March 1999 | |||
| Pos | Player | To | Fee | Date | |
|---|---|---|---|---|---|
| FW | Free | 31 May 1998 | |||
| MF | Free | 31 May 1998 | |||
| FW | Free | 31 May 1998 | |||
| FW | Free | 31 May 1998 | |||
| DF | Jason Heffernan | Released | 31 May 1998 | ||
| DF | Free | 31 May 1998 | |||
| DF | Free | 31 May 1998 | |||
| FW | Free | 1 June 1998 | |||
| GK | Retired | 3 July 1998 | |||
| MF | Free | 3 July 1998 | |||
| DF | Free | 3 July 1998 | |||
| MF | Free | 7 July 1998 | |||
| GK | Free | 31 August 1998 | |||
| DF | Loan | 18 September 1998 | |||
| DF | Loan | 18 September 1998 | |||
| DF | Loan | 6 November 1998 | |||
| DF | £50k | 1 December 1998 | |||
| DF | Loan | 24 December 1998 | |||
| FW | Loan | 11 February 1999 | |||
| DF | £50k | 19 February 1999 | |||
| DF | Loan | 22 March 1999 | |||
| FW | Free | 22 March 1999 | |||
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