On 14 May at Chelyabinsk, an eastbound train bearing Legion forces, encountered a westbound train bearing Hungarians, who were loyal to Austria-Hungary and the Central Powers and who regarded Legion troops as traitors. An armed conflict ensued at close range, fueled by the rival nationalisms. The Legion defeated the Hungarian loyalists. In response, local Bolsheviks intervened, arrested some Legion troops. The Legion then attacked the Bolsheviks, storming the railway station, freeing their men, and effectively taking over the city of Chelyabinsk while cutting the Bolshevik rail link to Siberia.

This incident was eventually settled peacefully but it was used by the Bolshevik regime to order the disarmament of the Legion as the episode had threatened Yekaterinburg, 140 miles away, and sparked wider hostilities throughout Siberia, in which the Bolsheviks steadily lost control over the railway and the region: the Legion quickly occupied more cities on the Trans-Siberian Railway, including Petropavl, Kurgan, Novonikolaevsk, Mariinsk, Nizhneudinsk, and Kansk. Though the Legion did not specifically seek to intervene on the anti-Bolshevik side in the Russian Civil War and sought only to secure safe exit from Russia, Bolshevik defeat in Siberia enabled anti-Bolshevik or White Russian officers' organizations to seize the advantage, overthrowing Bolsheviks in Petropavl and Omsk. In June, the Legion, having informally sided against the Bolsheviks for protection and convenience, captured Samara, enabling the first anti-Bolshevik local government in Siberia, the Komuch, formed on 8 June. On 13 June, Whites formed the Provisional Siberian Government in Omsk. 

On 3 August, Japanese, British, French, and American troops landed at Vladivostok. The Japanese sent about 70,000 into the country east of Lake Baikal. Yet, by the autumn of 1918, the legion no longer played an active part in the Russian civil war. After the coup against the Provisional All-Russian Government, and the installment of Alexander Kolchak's military dictatorship, the Czech's were withdrawn from the front, and assigned the task of guarding the Trans-Siberian Railway.

In the autumn, the Red Army counterattacked, defeating the Whites in western Siberia. In October, Czechoslovakia was proclaimed newly independent. In November, Austria-Hungary collapsed and World War I ended, intensifying the desire of Legion members to exit Russia, particularly as the new Czechoslovakia faced opposition by, and armed conflict with, its neighbors. In early 1919, Legion troops began to retreat to the Trans-Siberian Railway. On 27 January 1919, Legion commander Jan Syrový claimed the Trans-Siberian Railway between Novonikolaevsk and Irkutsk as a Czechoslovak zone of operation, interfering with White Russian efforts in Siberia.

Early in 1920 in Irkutsk, in return for safe transit eastward for Czechoslovak trains, Syrový agreed to hand over Aleksandr Kolchak to the representatives of the Red Political Centre, who executed Kolchak in February. Because of this, and also because of an attempted rebellion against the Whites, organized by Radola Gajda in Vladivostok on 17 November 1919, the Whites impotently accused the Czechoslovaks of treason. Between December 1919 and September 1920, the Legion evacuated by sea from Vladivostok.