Vláčil worked in a studio of Czechoslovak military film during his compulsory military service. He was in the military from 1951 to 1958. He met with cinematographer Jan Čuřík with whom he frequently collaborated during his career. He also met another director Karel Kachyňa. Vláčil's short films made in the military studio were mostly instructory and propagandist. His first film was a 1953 short Vzpomínka that commemorated deceased communist president Klement Gottwald. Another of his film shorts is a documentary Posádka na štítě that is about meteorologists working on Lomnický štít. The film shows contrast between a man and mountains. Vláčil also participated in the filmmaking of other directors. In 1955, Vláčil participated as an adviser in the making of the war film, Tank Brigade, coordinating battle scenes. His last military short was an instructory and motivational film Sebeobrana. He also made a short film Clouds of Glass which is considered his finest creation while in the army. It is the only film that Vláčil made in the military and was not determined by politics or genre. Clouds of Glass won an award at the Documentary and Short Film Festival in Venice. Vláčil left the army in 1958.
