The Campeonato Brasileiro Série C 1999, the third level of the Brazilian National Football League, was played from 27 August to 23 December 1999. The competition had 36 clubs and two of them were promoted to Série B.

Fluminense finished the final phase group with most points and was declared 1999 Brazilian Série C champions, claiming the promotion to the 2000 Série B along with São Raimundo, the runners-up. However, with the creation of the Copa João Havelange, Fluminense was promoted directly to the equivalent of the Série A, the Group Blue, while five quarterfinalists (Serra, Náutico, Figueirense, Caxias and Americano), along with Brasil de Pelotas, Villa Nova (reached the second phase), Bangu, Fortaleza, Anapolina and CSA (eliminated in the first phase) were promoted to the Group Yellow.

Group A

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification
1	São Raimundo	10	7	1	2	21	8	+13	22	Qualified for the second stage
2	Rio Negro	10	6	2	2	24	10	+14	20
3	Ypiranga	10	5	0	5	19	26	−7	15
4	Castanhal	10	3	3	4	13	18	−5	12
5	Ji-Paraná	10	2	3	5	12	20	−8	9
6	Vasco da Gama-AC	10	1	3	6	11	18	−7	6

Group B

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification
1	Botafogo-PB	10	6	1	3	19	10	+9	19	Qualified for the second stage
2	Moto Club	10	6	0	4	13	9	+4	18
3	Potiguar de Mossoró	10	6	0	4	14	11	+3	18
4	Picos	10	4	2	4	10	13	−3	14
5	Fortaleza	10	4	1	5	16	15	+1	13
6	Tocantinópolis	10	1	2	7	8	22	−14	5

Group C

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification
1	Náutico	10	8	2	0	25	7	+18	26	Qualified for the second stage
2	Sergipe	10	5	2	3	11	12	−1	17
3	CSA	10	3	4	3	14	9	+5	13
4	Itabaiana	10	3	3	4	14	16	−2	12
5	Unibol	10	2	4	4	13	16	−3	10
6	Fluminense de Feira	10	1	1	8	8	25	−17	4

Group D

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification
1	Serra	10	7	1	2	14	4	+10	22	Qualified for the second stage
2	Fluminense	10	7	0	3	17	10	+7	21
3	Villa Nova	10	5	3	2	13	10	+3	18
4	Anapolina	10	4	2	4	11	9	+2	14
5	Goiânia	10	2	2	6	8	15	−7	8
6	Dom Pedro II	10	0	2	8	6	21	−15	2

Group E

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification
1	Americano	10	6	2	2	13	8	+5	20	Qualified for the second stage
2	Juventus	10	5	2	3	10	8	+2	17
3	Atlético Goianiense	10	4	2	4	15	11	+4	14
4	Bangu	10	3	5	2	10	7	+3	14
5	Juventude-MT	10	4	1	5	8	10	−2	13
6	Operário-MS	10	0	4	6	10	22	−12	4

Group F

Pos	Team	Pld	W	D	L	GF	GA	GD	Pts	Qualification
1	Caxias	10	5	4	1	20	8	+12	19	Qualified for the second stage
2	Figueirense	10	5	4	1	23	14	+9	19
3	Brasil de Pelotas	10	5	1	4	16	12	+4	16
4	Rio Branco-PR	10	4	3	3	17	17	0	15
5	América-SP	10	2	3	5	13	25	−12	9
6	Volta Redonda	10	1	1	8	9	22	−13	4

Teams			Scores
Team 1	Points	Team 2	1st leg	2nd leg	3rd leg	Agg.
Figueirense	6:0	Rio Negro	3:1	2:0	—	5:1
Ypiranga	0:6	Náutico	0:3	0:1	—	0:4
Potiguar de Mossoró	3:6	Americano	2:0	0:3	0:2	2:5
Sergipe	6:0	Botafogo-PB	2:0	3:0	—	5:0
Juventus	1:7	Caxias	0:0	0:3	0:3	0:6
Moto Club'	1:7	Fluminense	1:1	0:1	1:2	2:4
Villa Nova	3:6	Serra	3:1	0:1	1:3	4:5
Brasil de Pelotas	0:6	São Raimundo	0:1	1:4	—	1:5

Teams			Scores
Team 1	Points	Team 2	1st leg	2nd leg	3rd leg	Agg.
Americano	1:7	Fluminense	1:1	0:4	1:2	2:7
Sergipe	4:4	Náutico	2:0	1:1	1:5	4:6
Caxias	4:4	Serra[a]	3:1	1:3	0:0	4:4
Figueirense	4:4	São Raimundo[b]	3:1	0:2	1:1	4:4

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