A total of 12 teams participate in this edition of the Second League.
New members are FK Mornar Bar who was relegated from 2015–16 Montenegrin First League, and winners of Montenegrin Third League playoffs - FK Čelik Nikšić and FK Otrant-Olympic Ulcinj.
During the first two rounds, each team played each other once home-and-away for a total of 22 games.
The pairings of the third round were then set according to the standings after the first two rounds, giving every team a third game against each opponent for a total of 33 games per team.
The runners-up and third-placed team in this season's league, Rudar Pljevlja and Petrovac respectively, will each pair off against the eighth and ninth-placed teams from the 2016–17 Montenegrin First League in the relegation play-offs, to be played over two legs.