[1] The company's activities primarily involved the movement of rail freight, particularly that of Russian oil products to the ice-free Estonian ports on the Baltic Sea; passenger services were typically provided by separate operators that ran upon Eesti Raudtee's infrastructure via a series of track access agreements.

[4][5] As a result of the privatization, new management structures were promptly introduced to the company along with considerable investment aimed at instituting international best practices, amongst other goals.

In July 2005, Baltic Rail Services issued a notice of dispute to the Estonian government that claimed there had been a breach of bilateral investment treaties.

[19] During December 2020, a joint venture of Spanish engineering companies Ardanuy Ingeneria and Ayesa Ingenieria y Arquitectura were awarded a €3.7m contract to produce the technical requirements and preliminary designs of an 25 kV 50 Hz electrification programme covering almost the entirety of Estonia's unelectrified railway network.

[21] As one part of this initiative, a new multimodal freight terminal directly connected to Muuga Harbour was constructed, facilitating the transshipping of goods between the sea and the Estonian railway network.