Kaunas sits where the Nemunas and Neris rivers meet, the kind of confluence that made medieval cities and the kind of crossroads that ensured medieval wars. The city was first mentioned in writing in 1361. In 1408, Vytautas the Great granted Magdeburg rights, and Kaunas began governing itself as a free trading city; by 1441 it had become a Hanseatic League outpost on the eastern edge of that German trading network. The first Kaunas Castle held the river junction against the Teutonic Knights. By the late sixteenth century the city was one of the major trade hubs of the Polish-Lithuanian Commonwealth. Then came the long bad century: Russian invasions in 1655, Swedish armies in the Great Northern War, plagues, fires, and slow economic decline. After the Partitions of the Commonwealth in 1795, Kaunas became Russian Imperial territory, and the bishopric of Samogitia eventually moved here in 1864 to bring it under closer imperial supervision.

When the Russian Empire collapsed in 1917 and Lithuania declared independence in 1918, Vilnius was the obvious capital. But Polish forces took Vilnius in 1920 and held it for nearly two decades. Kaunas, the only major Lithuanian city outside Polish control, became Lithuania's working capital almost by default. The Constituent Assembly first met here on May 15, 1920. The Bank of Lithuania moved in. Government ministries took over former Russian buildings and quickly outgrew them. Money poured into construction: between roughly 1922 and 1939, more than ten thousand new buildings went up. The city's footprint expanded by 7.1 times. The population grew from around 18,000 to about 154,000. Architects designed the Vytautas the Great War Museum, the M. K. Čiurlionis National Art Museum, the Kaunas Central Post Office with its Lithuanian-folk-style curved canopy, the white-and-glass Pasaka and Romuva cinemas. The whole city became an essay on how to build a modern country quickly, in a style that was self-consciously Lithuanian and self-consciously twentieth-century at the same time.

Two interwar Kaunas stories sit beside each other. In 1933, Lithuanian-American pilots Steponas Darius and Stasys Girėnas flew a single-engine Bellanca named Lituanica nonstop from New York toward Kaunas; they made it to Germany, within hours of home, before crashing in a forest in what is now Poland. Their plane lies in fragments at the Vytautas the Great War Museum. Their image appears on Lithuanian banknotes and street names across the country. Meanwhile, in the Slabodka district on the other bank of the Neris, the Slabodka Yeshiva was one of the most prestigious institutions of higher Jewish learning in Europe. Kaunas's Jewish community numbered between thirty-five thousand and forty thousand—roughly a quarter of the city's population—with nearly a hundred organizations, forty synagogues, four Hebrew high schools, Yiddish schools, a hospital, and the businesses that filled much of the city's commerce. Almost none of this would survive the next decade.

In June 1940, Soviet forces occupied Lithuania under the secret terms of the Molotov-Ribbentrop Pact. Mass arrests, deportations to Siberia, and executions began immediately. Then, on June 22, 1941, Germany invaded the Soviet Union, and within two days the Wehrmacht had reached Kaunas. The Lithuanian Activist Front and aligned anti-Communist groups began killing Jewish residents in the streets even before the German civil administration arrived; by late June 1941 thousands had died in the Kaunas pogrom. The Kovno Ghetto would soon hold twenty-nine thousand people. Almost all were murdered, most at the Ninth Fort of the old Tsarist fortress complex ringing the city. The Japanese consul Chiune Sugihara and the Dutch consul Jan Zwartendijk worked together in 1940 to issue more than two thousand transit visas to Jewish refugees through their tiny offices, defying both their governments and the closing window. The Sugihara House on Vaižganto Street is now a museum. Kaunas was liberated by the Red Army on August 1, 1944, and re-occupied as part of Soviet Lithuania.

Soviet rule lasted forty-six years. Armed Lithuanian partisans fought in the forests until 1953. After military resistance ended, Kaunas continued as a center of cultural and religious dissent. The 1972 underground Catholic Chronicle of the Catholic Church in Lithuania began circulation in samizdat from a tiny printing operation. Lithuanians rioted in Kaunas in 1956 in solidarity with the Hungarian Uprising, and again in 1972 after the self-immolation of Romas Kalanta. On October 9, 1988, the Lithuanian flag was raised above the tower of the Vytautas the Great War Museum, the first such public flying of the tricolor since 1940. Independence came in 1990. Today Kaunas's population sits near three hundred thousand, with universities making it a self-styled student city—the QS Best Student Cities Rankings included it in 2024. The interwar architecture earned the European Heritage Label in 2015 and UNESCO World Heritage status in 2023. Kaunas served as European Capital of Culture in 2022. The city that was supposed to be temporary has become one of the more interesting modernist landscapes in Europe, partly because the people who built it were betting their country on it.