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