After the organization was destroyed in 1940 he fled the country and reached Mandatory Palestine, where he joined the 4th Czechoslovak Infantry Regiment, later reorganised as the Czechoslovak 11th Infantry Battalion (East), with Klapálek as its commander. The battalion fought in the Allied invasion of Syria and Lebanon in June and July 1941, and was then stationed on the Turkish border in August. From October to December 1941 the battalion fought in the defence of Tobruk under the command of the Polish Independent Carpathian Rifle Brigade. After its success at Tobruk the battalion was withdrawn to the rear. In May 1942 it was reorganised as the 200th Czechoslovak Light Anti-Aircraft Regiment, with Klapálek remaining as its commander. The regiment returned to the Levant, where it defended Haifa, Beirut and Az-Zeeb. Early in 1943 returned to Tobruk, which it defended until June. In July 1943 the regiment was transferred by sea to Great Britain, where it became part of the Czechoslovak Independent Armoured Brigade. Klapálek reached Britain in August and was made second-in-command of the brigade. From March 1944 Klapálek was stationed in London as head of Department I of the Ministry of Defence of the Czechoslovak government-in-exile. In August 1944 he transferred to the Soviet Union, where he commanded the 3rd Czechoslovak Independent Brigade. In September and October he led the brigade in the Battle of the Dukla Pass. In April 1945 Ludvík Svoboda promoted Klapálek to commander of the Czechoslovak 1st Army Corps. Klapálek successfully led the army in the Battle for Břest. On 17 May 1945 Klapálek returned to Prague on a white horse, leading the Czechoslovak soldiers who had fought abroad. Between 1945 and 1950 Klapálek served as an army officer in Prague. Along with Svoboda he supported the Communist coup d'état of February 1948, by establishing the Central office of the National Front (). He joined the Communist party in June 1948. In the political trials of Czechoslovak soldiers who had served with Western forces, Klapálek tried to protect his former colleagues. In 1949 he received a threatening letter encouraging him to leave the country. Klapálek did not take it seriously, but in 1951 he was sent into retirement. After the huge political trial of Rudolf Slánský in 1952, the Communists confiscated all of Klapálek's property and arrested him in Valdice prison.