Founded in 1993 as TKSK Tallinn (also known as TKSK Arsenal and later TKSK Visa), the team won six championships in a row between 1997 and 2002 under this name. In 2002 it was the first team to represent Estonia in the newly founded European Cup.
After four years in blank with Pärnu JK becoming the Meistriliiga's leading force, the team won three more titles in a row after becoming Levadia Tallinn's women section in 2007. In 2009 Levadia won its first national double as it also won the third edition of the national cup.
In 2010 Levadia was second to Pärnu, while in 2011 it was also overcome by Flora Tallinn, ending third 27 points from Pärnu.