After the Russian Empire lost the Crimean War, the importance of use of tactical use of modern inventions, as well as railways. In February 1851 the Government of Russia made a decision to build the Saint Petersburg – Warsaw Railway line. Starting from 1858 the line connecting Saint Petersburg and Warsaw was being built. In the territory of Lithuania, the construction of the railway section Daugavpils–Vilnius–Grodno including the branch Lentvaris–Kaunas–Kybartai (Virbalis) was started in spring 1859. The first railway stations in Lithuania were constructed on this line (21 stations): the super class stations in Lentvaris and Virbalis, as well as the first class stations in Kaunas and Vilnius. Due to the hilly and unfavorable for the direct rail passage terrain around Kaunas' centre, the Kaunas Railway Tunnel and largest in Lithuania railway bridge over the Nemunas river were constructed. On the 15 August 1861 the first train left Kaunas and reached Lentvaris. Kaunas railway station was officially opened on 21 February 1862. In 1944, the Station was bombed by the withdrawing German army.
The present-day Kaunas railway station was built on the foundation of the old station and designed by architect P. Ashastin. Its architecture was based on the principles of classicism: strict symmetry, separate and large-scale inner spaces, horizontally continued shape, massive valls and centrally oriented stairs. The station was reconstructed between 2005 and 9 April 2008.