Shortly before Christmas 1938, Winton was planning to travel to Switzerland for a skiing holiday. Following a call for help from Marie Schmolka and Doreen Warriner, he decided instead to visit Prague and help Martin Blake, who was in Prague as an associate of the British Committee for Refugees from Czechoslovakia, then in the process of being occupied by Germany, and had called Winton to ask him to assist in Jewish welfare work. Alongside the Czechoslovak Refugee Committee, the British and Canadian volunteers such as Winton, Trevor Chadwick, and Beatrice Wellington worked in organising to aid children from Jewish families at risk from the Nazis. Many of them set up their office at a dining room table in a hotel in Wenceslas Square. Altogether, Winton spent one month in Prague and left in January 1939, six weeks before the German occupation of Czechoslovakia. Other foreign volunteers remained, such as Chadwick, Warriner and Wellington. In November 1938, following Kristallnacht in Nazi-ruled Germany, the House of Commons approved a measure to allow the entry into Britain of refugees younger than 17, provided they had a place to stay and a warranty of £50 was deposited for their eventual return to their own country.
He also wrote to US politicians such as President Franklin D. Roosevelt, asking them to take more children. He said that two thousand more might have been saved if they had helped, but only Sweden took any besides those sent to Britain. The last group of 250, scheduled to leave Prague on 1 September 1939, were unable to depart. With Hitler's invasion of Poland on the same day, the Second World War had begun. Of the children due to leave on that train, only two survived the war.
The occasion marked the 70th anniversary of the final intended Kindertransport arranged by Winton, due to set off on 1 September 1939 but prevented by the outbreak of the Second World War that very day. At the train's departure, a memorial statue for Winton, designed by Flor Kent, was unveiled at the railway station.