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	SV Wehen Wiesbaden	10	380	148	105	127	522	466	549	1.4447	56	0.1474	0	0
2	VfL Osnabrück	9	342	144	95	103	459	379	527	1.5409	80	0.2339	2	0
3	SpVgg Unterhaching	10	380	131	101	148	517	553	494	1.3000	-36	-0.0947	0	1
4	Rot-Weiß Erfurt	10	380	130	98	152	455	511	488	1.2842	-56	-0.1474	0	1
5	Hansa Rostock	9	342	128	97	117	443	428	481	1.4064	15	0.0439	0	0
6	Preußen Münster	9	342	125	98	119	450	421	473	1.3830	29	0.0848	0	1
7	Hallescher FC	8	304	108	83	113	383	399	407	1.3388	-16	-0.0526	0	0
8	Chemnitzer FC	8	304	107	79	118	398	403	400	1.3158	-5	-0.0164	0	2
9	VfB Stuttgart II	8	304	96	81	127	372	411	369	1.2138	-39	-0.1283	0	1
10	SSV Jahn Regensburg	7	266	89	80	97	327	347	347	1.3045	-20	-0.0752	0	1
11	VfR Aalen	7	266	78	92	96	308	349	326	1.2256	-41	-0.1541	0	2
12	1. FC Heidenheim	5	190	91	48	51	301	222	321	1.6895	79	0.4158	0	0
13	FC Carl Zeiss Jena	7	266	76	77	113	314	425	305	1.1466	-111	-0.4173	0	2
14	TSV Eintracht Braunschweig	5	190	83	52	55	294	217	301	1.5842	77	0.4053	1	0
15	Dynamo Dresden	5	190	83	50	57	267	212	299	1.5737	55	0.2895	1	0
16	SV Wacker Burghausen	6	228	68	64	96	270	345	268	1.1754	-75	-0.3289	0	1
17	Kickers Offenbach	5	190	69	58	63	237	200	265	1.3947	37	0.1947	0	0
18	Holstein Kiel	5	190	67	64	59	241	201	265	1.3947	40	0.2105	0	1
19	Werder Bremen II	7	266	64	72	130	273	404	264	0.9925	-131	-0.4925	0	2
20	MSV Duisburg	4	152	68	49	35	226	163	253	1.6645	63	0.4145	1	0
21	1. FC Magdeburg	4	152	67	48	37	221	147	249	1.6382	74	0.4868	1	0
22	Würzburger Kickers	4	152	68	42	42	223	176	246	1.6184	47	0.3092	0	0
23	Fortuna Köln	5	190	62	48	80	222	287	234	1.2316	-65	-0.3421	0	1
24	Stuttgarter Kickers	5	190	59	54	77	221	264	231	1.2158	-43	-0.2263	0	2
25	Sonnenhof Großaspach	5	190	57	58	75	232	261	229	1.2053	-29	-0.1526	0	1
26	Karlsruher SC	3	114	62	33	19	182	94	219	1.9211	88	0.7719	1	0
27	SV Sandhausen	4	152	53	50	49	212	203	209	1.3750	9	0.0592	1	0
28	Arminia Bielefeld	3	114	56	32	26	185	130	200	1.7544	55	0.4825	1	0
29	SC Paderborn 07	3	114	57	24	33	196	128	195	1.7105	68	0.5965	0	0
30	FSV Zwickau	4	152	51	40	61	190	217	193	1.2697	-27	-0.1776	0	0
31	1. FC Saarbrücken	4	152	50	40	62	212	227	190	1.2500	-15	-0.0987	0	1
32	FC Erzgebirge Aue	3	114	51	33	30	142	105	186	1.6316	37	0.3246	0	0
33	Borussia Dortmund II	4	152	40	45	67	170	222	165	1.0855	-52	-0.3421	0	2
34	SV Meppen	3	114	44	31	39	167	157	163	1.4298	10	0.0877	0	0
35	Darmstadt 98	3	114	41	36	37	141	122	159	1.3947	19	0.1667	0	0
36	FC Bayern München II	3	114	36	35	43	139	157	143	1.2544	-18	-0.1579	0	1
37	Energie Cottbus	3	114	36	34	44	133	160	142	1.2456	-27	-0.2368	0	2
38	1. FSV Mainz 05 II	3	114	33	31	50	132	157	130	1.1404	-25	-0.2193	0	1
39	Sportfreunde Lotte	3	114	33	29	52	120	153	128	1.1228	-33	-0.2895	0	1
40	SV Babelsberg 03	3	114	32	31	51	115	160	127	1.1140	-45	-0.3947	0	1
41	FC Ingolstadt 04	2	76	35	22	19	133	86	127	1.6711	47	0.6184	0	0
42	1. FC Kaiserslautern	2	76	27	25	24	108	105	106	1.3947	3	0.0395	0	0
43	TSV 1860 München	2	76	28	21	27	111	106	105	1.3816	5	0.0658	0	0
44	KFC Uerdingen 05	2	76	26	18	32	87	116	96	1.2632	-29	-0.3816	0	0
45	Wuppertaler SV	2	76	21	20	35	76	106	83	1.0921	-30	-0.3947	0	1
46	RB Leipzig	1	38	24	7	7	65	34	79	2.0789	31	0.8158	0	0
47	1. FC Union Berlin	1	38	22	12	4	59	23	78	2.0526	36	0.9474	1	0
48	Fortuna Düsseldorf	1	38	20	9	9	54	33	69	1.8158	21	0.5526	0	0
49	Bayern Munich II	1	38	19	8	11	76	60	65	1.7105	16	0.4211	0	0
50	Kickers Emden	1	38	16	11	11	45	44	59	1.5526	1	0.0263	0	1
51	Waldhof Mannheim	1	38	13	17	8	52	47	56	1.4737	5	0.1316	0	0
52	Viktoria Köln	1	38	14	9	15	65	71	51	1.3421	-6	-0.1579	0	0
53	TuS Koblenz	1	38	13	10	15	38	46	49	1.2895	-8	-0.2105	0	1
54	SG Sonnenhof Großaspach	1	38	12	10	16	39	60	46	1.2105	-21	-0.5526	0	0
55	Rot Weiss Ahlen	1	38	11	9	18	45	69	42	1.1053	-24	-0.6316	0	1
56	SV Elversberg	1	38	10	10	18	32	54	40	1.0526	-22	-0.5789	0	1
57	Rot-Weiß Oberhausen	1	38	8	14	16	33	47	38	1.0000	-14	-0.3684	0	1
58	FSV Frankfurt	1	38	7	13	18	38	50	34	0.8947	-12	-0.3158	0	1
59	Alemannia Aachen	1	38	7	10	21	40	68	31	0.8158	-28	-0.7368	0	1