Carrillo was at the height of his medical career when he became acquainted with the Colonel Juan Domingo Perón, a patient at the Central Military Hospital with whom Carrillo shared long talks. Colonel Perón was the increasingly influential Labor Minister in the nationalist military regime that took power after the 1943 Argentine coup d'état, and during these talks persuaded Carrillo to help plan national health policies. Carrillo, at age 39, briefly served as Dean of the School of Medicine, acting as a go-between in a fierce, highly politized, Left-Right university conflict, which ultimately forced him to quit his faculty post.