The 40 teams are divided in eight groups of 5, playing within them in a double round-robin format. The two best ranked in each group at the end of 10 rounds will qualify to the Second Stage, which will be played in home-and-away system. Winners advance to Third Stage. The quarterfinal winners will be promoted to the Série C 2014. As there is no Série E, or fifth division, technically there will be no relegation. However, teams who were not promoted will have to re-qualify for Série D 2014 through their respective state leagues. The competition can also be considered as 4 mini-tournaments (Group 1+2;3+4;5+6;7+8) because according to the playoff-structure, exactly one team of each "mini-tournament" will be promoted.
* Aparecidense was excluded by the STJD, because in the second leg against Tupi, the Aparecidense's physio Ramildo De Silva invaded the field to save a goal at the 89th minute.[1]