After the independence of Estonia, the state-owned company Eesti Raudtee was founded on January 1, 1992, as the national railway company of Estonia. On August 31, 2001, 66% of the stock in the company was sold by the government to Baltic Rail Services (BRS), part-owned by Railroad Development Corporation.
Following an election in 2003, the new government changed the rules on open access rights and capped the level of track charges, which reduced the railway's viability. The railway was bought back by the state in a transaction completed in January 2007. In 2009 two new EVR's wholly owned subsidiaries were formed: EVR Infra, responsible for managing the railway infrastructure, and EVR Cargo, which took over the parent company's freight operations.