Archaeologists have found evidence of prehistoric human settlement in the area dating back to the Neolithic era. In the classical era, from the 3rd century BC Celtic migrations, the Boii (see Bohemia) and later in the 1st century Germanic tribes of Marcomanni and Quadi settled there. During the Migration Period around the 5th century, many Germanic tribes moved westwards and southwards out of Central Europe. In an equally significant migration, Slavic people from the Black Sea and Carpathian regions settled in the area (a movement that was also stimulated by the onslaught of peoples from Siberia and Eastern Europe: Huns, Avars, Bulgars and Magyars). Following in the Germans' wake, they moved southwards into Bohemia, Moravia, and some of present day Austria. During the 7th century the Frankish merchant Samo, supporting the Slavs fighting their Avar rulers, became the ruler of the first known Slav state in Central Europe. The Moravian principality arose in the 8th century (see Great Moravia). The Bohemian or Czech state emerged in the late 9th century when it was unified by the Přemyslid dynasty. The kingdom of Bohemia was a significant regional power during the Middle Ages. It was part of the Holy Roman Empire during the entire existence of this confederation.

Religious conflicts such as the 15th century Hussite Wars and the 17th century Thirty Years' War had a devastating effect on the local population. From the 16th century, Bohemia came increasingly under Habsburg control as the Habsburgs became first the elected and then hereditary rulers of Bohemia. After the fall of the Holy Roman Empire, Bohemia became part of Austrian Empire and later of Austria-Hungary.

Following the collapse of the Austro-Hungarian Empire after World War I, the independent republic of Czechoslovakia was created in 1918. This new country incorporated regions of Bohemia, Moravia, Silesia, Slovakia and Carpathian Ruthenia (known as Subcarpathian Rus at the time) with significant German, Hungarian, Polish and Ruthenian speaking minorities Although Czechoslovakia was a unitary state, it provided what was at the time rather extensive rights to its minorities. However, it did not grant its minorities any territorial political autonomy, which resulted in discontent and strong support among some of the minorities to break away from Czechoslovakia. Adolf Hitler used the opportunity and, supported by Konrad Henlein's Sudeten German National Socialist Party, gained the largely German speaking Sudetenland through the 1938 Munich Agreement. Poland occupied Polish inhabited areas around Český Těšín. Hungary gained parts of Slovakia and Subcarpathian Rus as a result of the First Vienna Award in November 1938.

Slovakia and Subcarpathian Rus gained greater autonomy, with the state renamed to "Czecho-Slovakia" (The Second Republic; see Occupation of Czechoslovakia). Slovakia seceded in March 1939 and allied itself with Hitler's coalition. The remaining Czech territory was occupied by Germany, transformed it into the so-called Protectorate of Bohemia and Moravia. The Protectorate was proclaimed part of the Third Reich, and President and Prime Minister were subordinate to the Nazi Reichsprotektor ("imperial protector"). Subcarpathian Rus declared independence as the Republic of Carpatho-Ukraine on 15 March 1939 but was invaded by Hungary the same day and formally annexed on 16 March. Approximately 390,000 Czechoslovak citizens, including 83,000 Jews, were killed or executed, and hundreds of thousands of others were sent to prisons and concentration camps or as forced labour. A Nazi concentration camp existed at Terezin to the north of Prague. There was Czech resistance to Nazi occupation both home and abroad, most notably with the assassination of leading Nazi leader Reinhard Heydrich in Prague suburbs on May 27, 1942. The Czechoslovak government-in-exile and its army fighting against the Germans were acknowledged by Allies (Czechoslovak troops fought in Great Britain, North Africa, Middle East and Soviet Union). The occupation ended on 9 May 1945 with the arrival of Soviet and American armies and the Prague uprising.

In 1945-46 almost the entire German minority of Czechoslovakia, about 2.7 million people, were expelled to Germany and Austria. During this time, thousands of Germans were held in prisons, detention camps, and used as forced labour. In the summer of 1945, there were several massacres. Only 250,000 Germans who had been active in the resistance against the Nazis or were necessary for the economy were not expelled, though many of them emigrated later. Following a Soviet-organised referendum, the Subcarpathian Rus has never returned under Czechoslovak rule and became part of the Ukrainian SSR, as the Zakarpattia Oblast in 1946.

Czechoslovakia uneasily tried to play the role of a "bridge" between the West and East. However, the Communist Party of Czechoslovakia rapidly increased in popularity, particularly because of a general disappointment with the West (due to the pre-war Munich Agreement) and a favourable popular attitude towards the Soviet Union (due to the Soviets' role in liberating Czechoslovakia from German rule). In the 1946 elections, with 38% of the votes, the Communists became the largest party in the Czechoslovak parliament. They formed a coalition government with other parties of the National Front, and moved quickly to consolidate power. The decisive step took place in February 1948. During a series of events characterized by Communists as a "revolution" and by anti-Communists as a "takeover", the Communist People's Militias secured control of key locations in Prague, and a new, all-Communist government was formed.

For the next forty-one years, Czechoslovakia was a Communist state within the eastern bloc (see Czechoslovakia: 1948-1989). This period was marked by a variety of social developments. The Communist government completely nationalized the means of production and established a command economy. The economy grew rapidly during the 1950s and 1960s, but slowed down in the 1970s with increasing problems during the 1980s. The political climate was highly repressive during the 1950s (including numerous show trials), but became more open and tolerant in the 1960s, culminating in Alexander Dubček's leadership in the 1968 Prague Spring that tried to create "socialism with a human face" and perhaps even introduce political pluralism. This was forcibly ended by 21 August 1968 Warsaw Pact invasion. From then until 1989, the political establishment returned to censorship of opposition, though using more "carrot" than "whip" policy to ensure the populace's passivity.

In November 1989, Czechoslovakia returned to democracy through a peaceful "Velvet Revolution". However, Slovak national aspirations strengthened until on January 1, 1993, the country peacefully split into the independent Czech Republic and Slovakia. Both countries went through economic reforms and privatisations, with the intention of creating a market economy.

From 1991 the Czech Republic (originally as part of Czechoslovakia, and now in its own right) has been a member of the Visegrad Group and from 1995 of the OECD. The Czech Republic joined NATO on March 12, 1999 and the European Union on May 1, 2004.