The 2012–13 Estonian Cup was the 23rd season of the Estonia's most prestigious football knockout tournament.
Flora won the competition after they defeated Kalju 3–1 in the final.
The draw was made by Estonian Football Association on 26 May 2012, before the 2011–12 final of the same competition.
FC Helios is the only team that takes part from Rahvaliiga (RL) — a league organized by Estonian Football Association, but not part of the main league system.
Tammeka got bye to the semi-finals as the eighth quarter-finalist, Viljandi, was disbanded after the 2012 league season.