The infrastructure of Estonian Railways includes 61 stations, three of which are border stations: two at the Russian border (Narva-Ivangorod and Koidula-Petchory) and one at the Latvian border (Valga-Valka).

The total capacity of border stations is 56 pairs of trains in 24 hours: 38 pairs of trains on the Russian route and 18 trains on the Latvian route. Both border stations and intermediate stations have 1,500 meter station tracks, enabling servicing of long freight trains.