Vaginov was born in St. Petersburg in 1899. His mother was the daughter of a wealthy Siberian businessman and landowner. His father, a high-ranking police official, was descended from Germans who came to Russia in the 17th century. During the First World War, the family name was changed from Wagenheim (Russian: Вагенгейм) and given a Russian ending. Following his father's wishes, Vaginov studied law. During the Civil War, Vaginov served in the Red Army, both at the Polish front and east of the Urals. He returned to Petrograd and, after being demobilized, continued studies in the arts and humanities. In 1926 he married Alexandra Ivanovna Fedorova. She and Vaginov were both part of a group of writers who gathered about the poet, world traveler and decorated war hero Nikolai Gumilyov, who was shot in 1921, after being wrongly accused of plotting against the government.
Konstantin Vaginov died of tuberculosis in 1934.