The 1998–99 season was the 113th season in the history of Luton Town F.C. It was Luton Town's 78th consecutive season in the Football League, and their 81st overall. It was their third consecutive season in the Football League Third Division.

During the 1998–99 English football season, Luton Town F.C. competed in the Football League Second Division. Having finished strongly to narrowly avoid relegation in the previous season Luton Town carried their good form into the start of the 1999 season. Their bright start to the season saw them competing for a playoff spot as well as progressing to the quarter-final of the League Cup. However their defeat to Sunderland in the League Cup coincided with a run of only 1 win in 12 league games which saw Luton Town drop out of playoff contention.

Luton Town's season took a turn for the worse in February. Even though they suffered 7 defeats in 8 league games, the club's situation off the pitch was even more dire. Luton's long-running plan for a multi-purpose 'Kohlerdome' stadium, to be named after chairman David Kohler, was finally rejected by the Department of the Environment. As a result, David Kohler announced on 19 February that he would be resigning as chairman of the club. Kohler spent the next month trying to sell the club. But having failed to agree a price with fellow directors, including Cliff Bassett, for his share of the club, Kohler and the board decided there was no option but to appoint receivers. Buchler Phillips were appointed and Luton Town went into receivership on 20 March.

A strong finish to the season on the back of a loan striker's goals, this time Tony Thorpe, had shades of the 1998 season and Rory Allen's legendary contribution. Thorpe's 4 goals in the final 4 games saw Luton pick up 9 points and ensure their safety for another season.

Luton Town's score comes first^[1]

^[2] Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply. Players may hold more than one non-FIFA nationality.

No. Pos. Nation Player — GK  ENG Nathan Abbey — GK  ENG Kelvin Davis — GK  ENG Scott Ward — DF  SCO Graham Alexander — DF  ENG Steve Davis — DF  ENG Sean Dyche — DF  BRB Emmerson Boyce — DF  ENG Marvin Johnson — DF  ENG Gavin McGowan — DF  ENG James Ayres — DF  ENG Mitchell Thomas — DF  ENG Alan White — DF  ENG Matthew Taylor — DF  IRL Gary Doherty — DF  SCO Stuart Fraser — DF  ENG Chris Willmott — MF  ENG Sean Evers — MF  ENG Paul McLaren

No. Pos. Nation Player — MF  SCO Ray McKinnon — MF  ENG Paul Showler — MF  ENG Andre Scarlett — MF  SCO Michael McIndoe — MF  ENG Matthew Spring — MF  ENG Gerry Harrison — MF  WAL Simon Davies — MF  ENG Jimmy Cox — MF  ENG Kofi Nyamah — FW  ENG Stuart Douglas — FW  ENG Andrew Fotiadis — FW  IRL Liam George — FW  JAM Dwight Marshall — FW  ENG Tony Thorpe — FW  NIR Phil Gray — FW  FRA Hervé Bacqué — FW  COD Trésor Kandol — FW  CIV Landry Zahana-Oni

Pos.	Name	League		FA Cup		League Cup		FL Trophy		Total
		Apps	Goals	Apps	Goals	Apps	Goals	Apps	Goals	Apps	Goals
MF	Matthew Spring	45	3	1 (1)	0	7	0	0	0	53 (1)	3
GK	Kelvin Davis	44	0	2	0	7	0	0	0	53	0
DF	Marvin Johnson	42	0	1	0	7	1	0	0	50	1
FW	Stuart Douglas	42	9	1 (1)	0	6	2	0	0	49 (1)	11
FW	Phil Gray	32 (3)	8	2	2	6	3	0	0	40 (3)	13
DF	Gavin McGowan	27 (4)	0	2	0	7	0	0	0	36 (4)	0
DF	Alan White	18 (15)	1	1	0	0 (3)	0	1	0	20 (18)	1
MF	Graham Alexander	28	4	2	0	7	2	0	0	37	6
MF	Sean Evers	27	3	2	0	7	1	1	0	37	4
MF	Ray McKinnon	27	3	2	0	7	1	1	0	35 (2)	2
DF	Mitchell Thomas	26 (6)	0	0	0	3	0	0	0	29 (6)	0
MF	Paul McLaren	14 (9)	0	2	0	1 (3)	1	1	0	18 (12)	1
DF	Steve Davis	20	6	2	2	7	2	0	0	29	10
MF	Michael McIndoe	17 (5)	0	0 (2)	0	2 (1)	0	1	0	20 (8)	0
FW	Andrew Fotiadis	8 (13)	2	0	0	1 (2)	1	1	0	10 (15)	3
FW	Gary Doherty	5 (15)	6	1 (1)	0	0 (1)	0	0 (1)	0	6 (18)	6
MF	Gerry Harrison	14	0	0	0	0	0	1	0	15	0
DF	Sean Dyche	14	1	0	0	0	0	1	0	15	1
DF	Chris Willmott	13 (1)	0	0	0	0	0	0	0	13 (1)	0
FW	Liam George	6 (6)	0	0	0	0 (2)	0	0	0	6 (8)	0
FW	Hervé Bacqué	2 (5)	0	0	0	1 (2)	0	1	0	4 (7)	0
MF	Jimmy Cox	3 (5)	0	0	0	1 (1)	0	0	0	4 (6)	0
DF	Stuart Fraser	5 (3)	0	0	0	0	0	1	0	6 (3)	0
FW	Tony Thorpe	7 (1)	4	0	0	0	0	0	0	7 (1)	4
FW	Landry Zahana-Oni	4 (4)	0	0	0	0	0	0	0	4 (4)	0
MF	Andre Scarlett	2 (4)	1	0 (1)	0	0	0	0 (1)	0	2 (6)	1
FW	Dwight Marshall	3 (1)	1	0	0	3	0	0	0	6 (1)	1
FW	Trésor Kandol	2 (2)	0	0	0	0	0	0 (1)	0	2 (3)	0
GK	Nathan Abbey	2	0	0	0	0	0	1	0	3	0
MF	Paul Showler	2 (1)	0	0	0	0	0	0	0	2 (1)	0
MF	Simon Davies	2	0	0	0	0	0	0	0	2	0
DF	Emmerson Boyce	1	0	0	0	0	0	1	0	2	0
MF	Kofi Nyamah	0	0	1	0	0 (1)	0	0	0	1 (1)	0