A draw for the first round was held by CBF on January 11, 2016. The 80 qualified teams were divided in eight groups (A-H) with 10 teams each. That division was based on the 2016 CBF ranking and the matches were drawn from the respective pots: A vs. E; B vs. F; C vs. G; D vs. H. The lower ranked teams of each match hosted the first leg. Before the round of 16 there was another draw including the six teams that directly qualified for that round. All draws were at CBF headquarters in Rio de Janeiro.
A draw by CBF was held to set the matches for the round of 16. The 16 qualified teams were divided in two pots (1-2). Teams from pot 1 were the six teams directly qualified to the round of 16, the five teams that competed at the 2016 Copa Libertadores and the best placed team in the 2015 Campeonato Brasileiro Série A not taking part in the 2016 Copa Libertadores, plus the two highest CBF ranked teams in 2016 qualified via the third round. Pot 2 was composed of the other teams that qualified through the third round. Each pot was divided into 4 pairs according to the CBF ranking. That division made sure that each team within a pair would not face each other before the finals as they would be placed in opposite sides of the bracket. The draw also decided the home team of the round of 16. The following stages had additional draws to determine the order of the matches as the tournament advanced. All draws will be held at CBF headquarters in Rio de Janeiro.
^"Imperatriz conquista segundo título da história ao vencer Sampaio Corrêa" (in Portuguese). Globoesporte.com. 2 May 2015. Enquanto o Sampaio vai jogar a Série B do Campeonato Brasileiro, o Imperatriz se prepara para jogar o Campeonato Brasileiro Série D e vai tentar o acesso para a Série C de 2016, o que seria outro feito inédito na história do clube. Ambos os times estão também, em 2016, na Copa do Brasil e Copa do Nordeste.