Kybartai was founded during the reign of Sigismund I the Old by the colonization efforts of his wife, Queen Bona Sforza.

When in 1861 a branch of the Saint Petersburg–Warsaw Railway was built from Vilnius to the Prussian border, where it was linked to the Prussian Eastern Railway, the Russian border station near the village of Kybartai was named after the neighbouring town of Verzhbolovo (Вержболово), Lithuanian Virbalis, German Wirballen.

Late in the evening of 15 June 1940, when the Soviet Army invaded Lithuania, President Smetona fled from Kybartai to Germany after crossing the Liepona stream.

[2] On 23 June 1940, the Kybartai Acts [lt] were signed actually in Bern, but dated retrospectively by 15 June supposedly in Kybartai, marking the formal transfer of power to the so-called Provisional Government of Lithuania when Lithuania was occupied by the Soviet Army.

On June 30, 1941, an Einsatzgruppe of Germans and a few Lithuanian policemen perpetrated a mass execution of the local Jewish population.