The all-time table uses three points for a win and one point for a draw, and does not consider point deductions

Rank	Team	Seasons	G	W	D	L	GF	GA	Pts	Pts/Game	+-	+-/game	Champions	Relegated
1	FC Levadia Tallinna II	11	388	245	76	67	1032	386	811	2.0902	646	1.6649	0	0
2	FC Flora Tallinn II	9	324	170	56	98	664	416	566	1.7469	248	0.7654	0	1
3	FC Valga	9	278	119	39	120	472	539	396	1.4245	-67	-0.2410	1	0
4	FC Kuressaare	7	206	109	32	65	450	324	359	1.7427	126	0.6117	1	0
5	Kiviõli FC Irbis	7	252	97	46	109	496	555	337	1.3373	-59	-0.2341	0	1
6	Pärnu linnameeskond	8	258	89	51	118	476	518	318	1.2326	-42	-0.1628	1	2
7	FC Lootus Kohtla-Järve	7	214	97	27	90	412	400	318	1.4860	12	0.0561	1	0
8	JK Tervis Pärnu	8	240	85	25	130	406	604	280	1.1667	-198	-0.8250	0	3
9	Rakvere JK Tarvas	6	216	77	35	104	341	463	266	1.2315	-122	-0.5648	0	1
10	JK Tallinna Kalev	4	144	76	31	37	338	238	259	1.7986	100	0.6944	1	0
11	FC Ajax Lasnamäe	4	144	70	30	44	314	200	240	1.6667	114	0.7917	0	0
12	FC TVMK II Tallinn	5	172	63	23	86	302	363	212	1.2326	-61	-0.3547	0	1
13	FC Maardu	4	112	62	19	31	338	182	205	1.8304	156	1.3929	1	0
14	JK Merkuur Tartu	5	126	45	22	59	204	267	157	1.2460	-63	-0.5000	0	1
15	JK Kalev Sillamäe	5	134	45	20	69	190	257	155	1.1567	-67	-0.5000	0	3
16	FC Infonet	2	72	45	16	11	195	80	151	2.0972	115	1.5972	1	0
17	FC Puuma	4	144	37	28	79	208	372	139	0.9653	-164	-1.1389	0	2
18	JK Tulevik Viljandi	3	100	38	23	39	130	154	137	1.3700	-24	-0.2400	0	0
19	FC Elva	5	164	34	22	108	183	381	124	0.7561	-198	-1.2073	0	3
20	Tallinna Jalgpalli Klubi	4	120	34	22	64	164	300	124	1.0333	-136	-1.1333	0	1
21	MC Tallinn	3	84	34	17	33	167	170	119	1.4167	-3	-0.0357	0	0
22	Tallinna JK Legion	3	108	31	17	60	164	261	110	1.0185	-97	-0.8981	0	0
23	JK Tulevik II Viljandi	3	108	28	24	56	138	214	108	1.0000	-76	-0.7037	0	0
24	Tartu SK 10	2	72	32	12	28	123	125	108	1.5000	-2	-0.0278	0	0
25	JK Kalju Nõmme	2	72	31	14	27	145	149	107	1.4861	-4	-0.0556	0	0
26	JK Tammeka Tartu	3	84	29	18	37	165	199	105	1.2500	-34	-0.4048	1	1
27	JK Dünamo Tallinn	3	92	30	12	50	155	224	102	1.1087	-69	-0.7500	0	1
28	Tartu JK Maag Tammeka II	2	72	25	21	26	111	102	96	1.3333	9	0.1250	0	0
29	Jõhvi FC Lokomotiv	2	72	26	13	33	115	121	91	1.2639	-6	-0.0833	0	1
30	JK Tammeka Tartu II	2	72	25	14	33	125	140	89	1.2361	-15	-0.2083	0	0
31	KSK-Vigri	2	42	26	9	7	98	40	87	2.0714	58	1.3810	0	0
32	Vändra JK Vaprus	2	72	23	15	34	121	127	84	1.1667	-6	-0.0833	0	1
33	FCA Estel Tallinn	2	56	23	7	26	135	111	76	1.3571	24	0.4286	0	0
34	JK Kalju Nõmme II	1	36	17	6	13	69	62	57	1.5833	7	0.1944	0	0
35	Paide linnameeskond	1	36	14	12	10	58	44	54	1.5000	14	0.3889	0	0
36	FC Levadia Pärnu	1	28	15	7	6	67	39	52	1.8571	28	1.0000	1	0
37	HÜJK Emmaste	1	28	12	4	12	43	50	40	1.4286	-7	-0.2500	0	0
38	FC Levadia Tallinna	1	14	9	5	0	29	7	32	2.2857	22	1.5714	1	0
39	Välk 494 Tartu	1	36	7	8	21	49	93	29	0.8056	-44	-1.2222	0	1
40	Muhumaa JK	1	28	8	3	17	35	79	27	0.9643	-44	-1.5714	0	1
41	JK Merkuur II Tartu	1	36	3	5	28	27	97	14	0.3889	-70	-1.9444	0	1