Name | Location (settlement, municipality, county) | Year of opening | Further info | Image |
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[1] | Tartu, Tartu municipality, Tartu County | | | |
| Aegviidu, Anija Parish, Harju County | 1870 | | |
| Aruküla, Raasiku Parish, Harju County | 1920 | | |
| Elva, Elva Parish, Tartu County | 1889 | | |
| Haapsalu, Haapsalu municipality, Lääne County | 1904 | Closed 1997 | |
| Hagudi, Rapla Parish, Rapla County | 1900 | | |
| Tallinn, Harju County | 1926 | | |
| Holvandi, Põlva Parish, Põlva County | 1931 | | |
| Kikka, Räpina Parish, Põlva County | 1931 | | |
| Jaanika, Saue Parish, Harju County | | | |
| Jäneda, Tapa Parish, Lääne-Viru County | 1870 | | |
| Tallinn, Harju County | 1923 | | |
| Jõgeva, Jõgeva Parish, Jõgeva County | 1878 | | |
| Jõhvi, Jõhvi Parish, Ida-Viru County | 1929 | | |
| Kaarepere, Jõgeva Parish, Jõgeva County | 1927 | | |
| Viru-Kabala, Vinni Parish, Lääne-Viru County | 1870 | | |
| Kadrina, Kadrina Parish, Lääne-Viru County | 1870 | | |
| Kärevere, Türi Parish, Järva County | 1900 | | |
| Kärkna, Tartu Parish, Tartu County | | | |
| Käru, Türi Parish, Järva County | 1900 | | |
| Kasemetsa, Saku Parish, Harju County | | | |
| Keava, Kehtna Parish, Rapla County | 1901 | | |
| Keeni, Otepää Parish, Valga County | 1894 | | |
| Kehra, Anija Parish, Harju County | 1876 | | |
| Keila, Harju County | 1870 | | |
| Kibuna, Saue Parish, Harju County | | | |
| Kiidjärve, Põlva Parish, Põlva County | 1931 | | |
| Kiisa, Saku Parish, Harju County | 1928 | | |
| Kiltsi, Väike-Maarja Parish, Lääne-Viru County | 1876 | | |
| Tartu, Tartu municipality, Tartu County | | | |
| Tallinn, Harju County | 2008[2] | | |
| Tallinn, Harju County | 1924 | | |
| Kiviõli, Lüganuse Parish, Ida-Viru County | 1920s | | |
| Klooga, Lääne-Harju Parish, Harju County | 1870 | | |
| Klooga, Lääne-Harju Parish, Harju County | | | |
| Kloogaranna, Lääne-Harju Parish, Harju County | 1960 | | |
| Kohila, Kohila Parish, Rapla County | 1900 | | |
| Kohtla-Nõmme, Toila Parish, Ida-Viru County | 1876 | closed in 2014 | |
| Kohtla-Nõmme, Toila Parish, Ida-Viru County | 2014 | | |
| Koidula, Setomaa Parish, Võru County | 2011 | | |
| Kulli, Raasiku Parish, Harju County | | | |
| Kulna, Lääne-Harju Parish, Harju County | 1928 | | |
| Tallinn, Harju County | 1932 | Unofficially opened in 1928 | |
| Lagedi, Rae Parish, Harju County | 1872 | | |
| Vikipalu, Anija Parish, Harju County | 1939 | 1957–2009 known as Vikipalu | |
| Kaasiku, Saue Parish, Harju County | | | |
| Laoküla, Lääne-Harju Parish, Harju County | | | |
| Lehtse, Tapa Parish, Lääne-Viru County | 1876 | | |
| Lelle, Kehtna Parish, Rapla County | 1900 | | |
| Tallinn, Harju County | | | |
| Tallinn, Harju County | 1928 | | |
| Mälivere, Kohila Parish, Rapla County | | | |
| Ädu, Otepää Parish, Valga County | 1919 | | |
| Männiku, Saku Parish, Harju County | 1916 | | |
| Piirsalu, Lääne-Nigula Parish, Lääne County | | closed | |
| Mustjõe, Anija Parish, Harju County | 1927 | | |
| Narva, Ida-Viru County | 1870 | | |
| Aegviidu, Anija Parish, Harju County | 1938 | | |
| Niitvälja, Lääne-Harju Parish, Harju County | | | |
| Tallinn, Harju County | 1872 | | |
| Nõo Nõo Parish, Tartu County | 1898 | | |
| Ollepa, Türi Parish, Järva County | 1900 | | |
| Olustvere, Põhja-Sakala Parish, Viljandi County | 1900 | | |
| Rõssa, Võru Parish, Võru County | 1931 | | |
| Kohtla-Järve, Ida-Viru County | 1870s | | |
| Tallinn, Harju County | 1915 | | |
| Laagri, Saue Parish, Harju County | 2008 | | |
| Paldiski, Lääne-Harju Parish, Harju County | 1870 | | |
| Palupera, Elva Parish, Tartu County | | | |
| Parila, Anija Parish, Harju County | | | |
| Pärnu, Pärnu municipality, Pärnu County | | closed | |
| | | now in the territory of Russia, formerly in Estonia | |
| Pedja, Jõgeva Parish, Jõgeva County | | | |
| Elva Elva Parish, Tartu County | 1887 | | |
| Piusa, Võru Parish, Võru County | 1930 | | |
| Põllküla, Lääne-Harju Parish, Harju County | | | |
| Põlva, Põlva Parish, Põlva County | 1931 | | |
| Puka, Otepää Parish, Valga County | 1889 | | |
| Püssi, Lüganuse Parish, Ida-Viru County | 1870 | | |
| Raasiku, Raasiku Parish, Harju County | 1870 | | |
| Tallinn, Harju County | 1926 | | |
| Rakke, Väike-Maarja Parish, Lääne-Viru County | 1876 | | |
| Rakvere, Lääne-Viru County | 1870 | | |
| Rapla, Rapla Parish, Rapla County | 1900 | | |
| Rebase, Kambja Parish, Tartu County | | | |
| Tõõraste, Kastre Parish, Tartu County | 1931 | | |
| Kadaka, Haapsalu municipality, Lääne County | | closed | |
| Riisipere, Saue Parish, Harju County | 1905 | | |
| Risti, Lääne-Nigula Parish, Lääne County | | closed | |
| Roobuka, Saku Parish, Harju County | | | |
| Külitse, Kambja Parish, Tartu County | 1923 | | |
| Ruusa, Räpina Parish, Põlva County | 1931 | | |
| Saku, Saku Parish, Harju County | 1900 | | |
| Tsirguliina, Valga Parish, Valga County | 1889 | | |
| Saue, Saue Parish, Harju County | 1872 | | |
| Sonda, Lüganuse Parish, Ida-Viru County | 1890 | | |
| Sürgavere, Põhja-Sakala Parish, Viljandi County | 1900 | | |
| Tabivere, Tartu Parish, Tartu County | 1877 | | |
| Taevaskoja, Põlva Parish, Põlva County | 1931 | | |
| Taikse, Türi Parish, Järva County | 1900 | | |
Tallinn Baltic Station | Tallinn, Harju County | 1870[3] | | |
| Tallinn, Harju County | | | |
| Tamsalu, Tapa Parish, Lääne-Viru County | 1876 | | |
| Tapa, Tapa Parish, Lääne-Viru County | 1870 | | |
| Tartu, Tartu municipality, Tartu County | 1876 | | |
| Tallinn, Harju County | 1933 | | |
| Tõravere Nõo Parish, Tartu County | | | |
| Turba, Saue Parish, Harju County | 1924 | reopened in 2019 | |
| Türi, Türi Parish, Järva County | 1900 | | |
| Uhti, Kambja Parish, Tartu County | | | |
| Tallinn, Harju County | 1900 | | |
| Ülenurme, Kambja Parish, Tartu County | 1931 | | |
| Laagri, Saue Parish, Harju County | 2008 | | |
| Vägeva, Jõgeva Parish, Jõgeva County | | | |
| Jaakna, Lääne-Nigula Parish, Lääne County | | closed; also known as Jaakna railway station | |
| Vaivara, Narva-Jõesuu municipality, Ida-Viru County | 1870 | | |
| Tallinn, Harju County | 2017 | | |
| Valga, Valga Parish, Valga County | 1887 | | |
| Valgemetsa, Põlva Parish, Põlva County | | | |
| Valingu, Saue Parish, Harju County | | | |
| Vana-Kuuste, Kambja Parish, Tartu County | | | |
| Soinaste, Kambja Parish, Tartu County | | closed in 2008 | |
| Vasalemma, Lääne-Harju Parish, Harju County | 1917 | | |
| Vastse-Kuuste, Põlva Parish, Põlva County | 1931 | | |
| Veriora, Räpina Parish, Põlva County | 1931 | | |
| Tallinn, Harju County | | | |
| Vilivere, Kohila Parish, Rapla County | | | |
| Viljandi, Viljandi County | 1897 | | |
| Võhma, Põhja-Sakala Parish, Viljandi County | 1900 | | |
| Võru, Võru County | 1889 | closed to passenger trafic in 2001 | | |