After 1919, Moravec served as an army officer in Plzeň and in 1928 he joined the military intelligence service and moved to Prague.

In the evening of 14 March 1939, he and 10 of his fellow intelligence officers secretly managed to fly away with the most valuable intelligence files and archives from Prague Ruzyně Airport to London Croydon Airport with a stopover in Rotterdam on ad hoc chartered KLM Douglas DC-3, as they knew in advance from their secret agents operating in Nazi Germany that the invasion leading to German occupation of Czechoslovakia was to be on 15 March 1939, at 6 a.m. Rescued files and archives were handed over to the British MI6 to be used against Germany.

He also planned the assassination of his namesake Emanuel Moravec, a traitor and Nazi collaborator who was also known as the "Czech Quisling".

František Moravec returned to Czechoslovakia in 1945 after the Nazi Germany defeat but left secretly again in 1948, shortly after the communist coup d'état.

On 24 April 2022, the dignified transfer of Moravec's remains from the United States to Czech Republic took place at Joint Base Andrews.