During the season, teams play each opponent twice, once at home and once away, for 26 matches.
At the end of the season, the winners of both divisions face each other in one final match to determine the champion of II liiga.
Two clubs from the bottom end of both divisions are relegated to the III liiga.
These teams replaced Tartu FC Santos II and Maardu United (dissolved), Põhja-Tallinna JK Volta (promoted) as well as Raasiku FC Joker and Tallinna JK Piraaja (transferred to II S/W liiga).
a – ineligible for promotion to Esiliiga B 2018 II S/W Liiga consists of 14 different teams.
These teams replaced FC Nõmme United, Pärnu Jalgpalliklubi and FC Flora U19 (all promoted), Saue JK Laagri, SK Imavere and Viimsi JK II.