In the first stage, 68 teams were divided into seventeen groups of four, organized regionally. The teams played home and away against the other three teams in their group, a total of six games. The winner of each group plus the best 15 runners-up qualified for the second stage. From the second stage on the competition was played as a knock-out tournament. The four semi-finalists qualified for the 2017 Campeonato Brasileiro Série C. The winners of the semifinals played the final over two legs to determine the champion.
The Second stage was a two-legged knockout tie, with the draw regionalised.
Qualification and draw
The 32 qualifiers were divided into two pots. Pot 1 contained the 16 best performing group winners. Pot 2 contained the worst performing group winner and the 15 qualifying group runners-up. In pot 1 the teams were numbered 1 to 16 in numerical order of the group they qualified from. In pot 2 the teams were numbered 17 to 32 in numerical order of the group they qualified from. In the case that one of the qualifying runners-up was from the same group as the worst performing group winner, both teams would be in pot 2 and the group winner would be numbered lower in sequence than the group runner-up. To keep the draw regionalised Team 1 would play Team 18, Team 2 would play Team 17 and this pattern was repeated throughout the draw. The higher numbered team would play at home in the first leg.
Ranking of group winners
Ranking of group winners to determine the worst performing team to be placed into pot 2 was achieved by comparing 1) Points gained 2) Most victories 3) Best goal difference 4) Most goals scored 5) Sort.
Team
1
Altos
16
5
17
22
Pot 1
2
Ceilândia
15
5
13
19
Pot 1
3
Volta Redonda
14
4
10
11
Pot 1
4
Atlético Acreano
14
4
8
15
Pot 1
5
São Raimundo
13
4
13
15
Pot 1
6
Ituano
13
4
10
15
Pot 1
7
Princesa do Solimões
13
4
6
11
Pot 1
8
São Bento
13
4
6
7
Pot 1
9
Caldense
13
4
5
6
Pot 1
10
Uniclinic
12
3
6
11
Pot 1
11
CSA
11
3
7
13
Pot 1
12
Globo
11
3
7
11
Pot 1
13
J. Malucelli
11
3
4
8
Pot 1
14
Sete de Setembro
11
3
3
9
Pot 1
15
Águia de Marabá
11
3
2
7
Pot 1
16
Internacional de Lages
10
3
4
8
Pot 1
17
Campinense
10
3
2
7
Pot 2
Ranking of group runners-up
Ranking of group runners-up to determine the 15 best performing teams to be placed into pot 2 was achieved by comparing 1) Points gained 2) Most victories 3) Best goal difference 4) Most goals scored 5) Sort.
The third stage was also a two-legged knockout tie, with the draw regionalised. The ties were predetermined from the second stage, with the winner of second stage tie 1 playing the winner of second stage tie 2, etc.
Ties
First team in the draw has home advantage in the second leg.
Final stage
The final stage was a two leg knockout competition with quarter-final, semi-final and final rounds. The draw for the quarter final was seeded based on the table of results of all matches in the competition for the qualifying teams. First would play eighth, second would play seventh, etc. The top four seeded teams would play the second leg at home. The four quarter-final winners were promoted to Série C for 2017. The draw for the semi final was seeded based on the table of results of all matches in the competition for the qualifying teams. First would play fourth, second would play third. The top two seeded teams would play the second leg at home. In the final, the team with the best record in the competition would play the second leg at home.
