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Northern Counties East
Football League
Division One
Season	1998–99
Champions	Harrogate Railway Athletic
Promoted	Brodsworth Miners Welfare; Harrogate Railway Athletic
Matches played	156
Goals scored	556 (3.56 per match)
	← 1997–98 1999–2000 →

Northern Counties East
Football League
Premier Division
Season	1998–99
Champions	Ossett Albion
Promoted	Ossett Town
Relegated	Pickering Town; Pontefract Collieries
Matches played	380
Goals scored	1,287 (3.39 per match)
	← 1997–98 1999–2000 →

The 1998–99 Northern Counties East Football League season was the 17th in the history of Northern Counties East Football League, a football competition in England.

Premier Division

The Premier Division featured 17 clubs which competed in the previous season, along with three new clubs.

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Promotion or relegation
1	Ossett Albion	38	23	5	10	86	50	+36	74
2	Ossett Town	38	22	7	9	76	44	+32	73	Promoted to the Northern Premier League Division One
3	Brigg Town	38	20	12	6	78	43	+35	72
4	Hallam	38	22	5	11	95	63	+32	71
5	North Ferriby United	38	19	12	7	92	50	+42	69
6	Liversedge	38	21	4	13	87	63	+24	67
7	Arnold Town	38	19	7	12	78	56	+22	64
8	Denaby United	38	15	12	11	66	60	+6	57
9	Garforth Town	38	15	9	14	74	70	+4	54
10	Buxton	38	14	10	14	54	53	+1	52
11	Selby Town	38	15	7	16	59	61	−2	52
12	Sheffield	38	15	6	17	55	58	−3	51
13	Armthorpe Welfare	38	13	11	14	46	50	−4	50
14	Glasshoughton Welfare	38	13	9	16	58	71	−13	48
15	Thackley	38	14	5	19	65	77	−12	47
16	Eccleshill United	38	12	6	20	56	74	−18	42
17	Staveley Miners Welfare	38	9	11	18	50	84	−34	36^[a]
18	Maltby Main	38	8	6	24	51	87	−36	28^[a]
19	Pontefract Collieries	38	7	7	24	37	86	−49	26^[a]	Relegated to Division One
20	Pickering Town	38	5	7	26	44	107	−63	22	Relegated to Division One

Source: fchd
Rules for classification: 1) points; 2) goal difference; 3) number of goals scored.
Notes:

^ ^a ^b ^c Staveley Miners Welfare, Maltby Main and Pontefract Collieries were deducted 2 points.

Division One featured 12 clubs which competed in the previous season, along with one new club:

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Promotion or relegation
1	Harrogate Railway Athletic	24	15	6	3	58	29	+29	51	Promoted to the Premier Division
2	Brodsworth Miners Welfare	24	13	3	8	52	42	+10	42	Promoted to the Premier Division
3	Glapwell	24	12	6	6	47	39	+8	42
4	Parkgate	24	12	5	7	61	32	+29	41
5	Borrowash Victoria	24	12	5	7	48	38	+10	41
6	Worsbrough Bridge Miners Welfare	24	9	6	9	49	42	+7	33
7	Hall Road Rangers	24	9	6	9	44	49	−5	33
8	Hatfield Main	24	10	3	11	27	47	−20	31^[a]
9	Louth United	24	9	3	12	37	33	+4	30
10	Yorkshire Amateur	24	6	7	11	41	49	−8	25
11	Tadcaster Albion	24	6	6	12	33	51	−18	24
12	Rossington Main	24	6	4	14	37	51	−14	22
13	Winterton Rangers	24	3	8	13	22	54	−32	17

Source: fchd
Rules for classification: 1) points; 2) goal difference; 3) number of goals scored.
Notes: