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The 1998–99 Liga Bet season saw Hapoel Hurfeish (champions of the North A division), Maccabi Hadera (champions of the North B division), Hapoel Kiryat Ono (champions of the South A division) and A.S. Ramat Eliyahu (champions of the South B division) win the title. The four clubs were placed in Liga Alef, which became the fourth tier upon the creation of the Israeli Premier League.

At the bottom, Hapoel Karmiel, Beitar Tiberias, Hapoel Bu'eine (from North A division), Hapoel Ilut, Maccabi Umm al-Fahm (from North B division), Maccabi Qalansawe, Hapoel Tel Mond, Maccabi Holon (from South A division) and Beitar Beit Shemesh (from South B division) were all placed in Liga Gimel, which became the sixth tier.

The rest of the clubs remained in Liga Bet, which became the fifth tier of the Israeli football league system.

North A division

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification
1	Hapoel Hurfeish	30	22	8	0	60	19	+41	74	Placed in Liga Alef
2	Hapoel Bnei Nazareth	30	22	5	3	75	22	+53	71	Placed in Liga Bet
3	Hapoel Tuba	30	16	8	6	51	27	+24	56
4	Maccabi Givat-Harakafot	30	14	6	10	48	43	+5	48
5	Maccabi Sektzia Ma'alot-Tarshiha	30	13	8	9	58	41	+17	47
6	Tzeirei Nahf	30	14	4	12	52	38	+14	43^[a]
7	Hapoel Sakhnin	30	13	4	13	47	49	−2	43
8	Hapoel Arraba	30	12	4	14	47	49	−2	40
9	Hapoel Kafr Sumei	30	11	7	12	54	47	+7	40
10	Ironi Nahariya	30	11	5	14	37	38	−1	38
11	Hapoel Dir Hanna	30	11	4	15	37	44	−7	37
12	Ironi I'billin	30	11	4	15	28	46	−18	37
13	Hapoel Bnei Kafr Yasif	30	10	6	14	40	50	−10	36
14	Hapoel Karmiel	30	8	10	12	35	44	−9	34	Placed in Liga Gimel
15	Beitar Tiberias	30	6	5	19	41	85	−44	23
16	Hapoel Bu'eine	30	2	0	28	7	75	−68	6

Source: rsssf.com
Notes:

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification
1	Maccabi Hadera	30	23	4	3	90	21	+69	73	Placed in Liga Alef
2	Hapoel Bir al-Maksur	30	22	4	4	78	30	+48	70	Placed in Liga Bet
3	Hapoel Nahliel	30	16	3	11	48	50	−2	51
4	Hapoel Daliyat al-Karmel	30	14	6	10	59	45	+14	48
5	Hapoel Arab Nujeidat	29	13	7	9	41	41	0	46
6	Hapoel Mo'atza Ezorit Galil Tahton	30	13	4	13	45	40	+5	43
7	Maccabi Ironi Tirat HaCarmel	30	13	4	13	41	45	−4	43
8	Ironi Zikhron Ya'akov	30	10	9	11	53	60	−7	39
9	Maccabi Beit She'an	30	10	8	12	51	58	−7	38
10	Maccabi Ironi Baqa al-Gharbiyye	30	11	4	15	54	72	−18	37
11	Hapoel Asi Gilboa	29	9	10	10	34	29	+5	37
12	Hapoel Fureidis	30	9	10	11	33	44	−11	37
13	Hapoel Reine	30	9	8	13	40	42	−2	35
14	Hapoel Barta'a	29	8	5	16	29	46	−17	29
15	Hapoel Ilut	30	8	3	19	32	56	−24	27	Placed in Liga Gimel
16	Maccabi Umm al-Fahm	29	3	5	21	24	73	−49	14	Placed in Liga Gimel

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification
1	Hapoel Kiryat Ono	30	20	6	4	58	25	+33	66	Placed in Liga Alef
2	Hapoel Herzliya	30	17	10	3	52	18	+34	61	Placed in Liga Bet
3	Beitar Kfar Saba	30	16	6	8	65	48	+17	54
4	Maccabi Bat Yam	30	14	7	9	31	31	0	49
5	M.M. Givat Shmuel	30	12	10	8	43	30	+13	46
6	Beitar Nes Tubruk	30	13	5	12	41	37	+4	44
7	Hapoel Azor	29	12	7	10	46	47	−1	43
8	Beitar Ramat Gan	30	10	9	11	45	41	+4	39
9	Hapoel Jaljulia	30	10	8	12	39	43	−4	38
10	Hapoel Tira	30	10	8	12	30	39	−9	38
11	Hapoel Mahane Yehuda	30	9	11	10	32	37	−5	38
12	Hapoel Ironi Hod HaSharon	30	11	4	15	45	43	+2	37
13	Maccabi Kafr Qasim	29	10	6	13	45	39	+6	36
14	Maccabi Qalansawe	30	8	7	15	33	44	−11	31	Placed in Liga Gimel
15	Hapoel Tel Mond	30	8	6	16	32	46	−14	30
16	Maccabi Holon	30	1	6	23	24	93	−69	9

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification
1	A.S. Ramat Eliyahu	26	19	6	1	47	14	+33	63	Placed in Liga Alef
2	Maccabi Shikun HaMizrach	25	15	6	4	55	27	+28	51	Placed in Liga Bet
3	Hapoel Marmorek	26	13	9	4	57	27	+30	48
4	Maccabi Ben Zvi	24	14	5	5	47	28	+19	47
5	Maccabi Jerusalem/Ma'ale Adumim	25	14	4	7	60	33	+27	46
6	Hapoel Ironi Eilat	26	10	1	15	63	60	+3	31
7	Maccabi Neve-Alon Lod	25	10	1	14	45	57	−12	31
8	Hapoel Bnei Lod	26	7	10	9	36	43	−7	31
9	Ironi Ofakim	24	8	6	10	40	38	+2	30
10	Hapoel Merhavim	26	8	5	13	43	48	−5	29
11	Hapoel Masos/Segev Shalom	26	7	8	11	35	46	−11	29
12	Maccabi Be'er Sheva	26	7	5	14	31	54	−23	26
13	Hapoel Ironi Be'er Ya'akov	25	6	4	15	38	50	−12	22
14	Beitar Beit Shemesh	22	2	2	18	19	91	−72	8	Placed in Liga Gimel

Hapoel Yehud (at the start of the season)^[1] and Hapoel Kiryat Malakhi (during the season) withdrew from the league.
Results of several matches are unknown