In the Russian Civil War, Naumenko fought on the White side. The British journalist Christopher Booker called Naumenko "a White Russian hero during the Civil War". Naumenko took part in the Ice March of the Volunteer Army under Kornilov in February–March 1918. On 18 February 1918, he was promoted to the rank of full colonel. By early March 1918, Naumenko was leading the Cossacks of the Kuban People's Republic into sporadic, but bitter clashes against the Red Army. Later in March 1918, Naumenko led the first joint operation between the Whites and the Kuban Host to take the "stanitsa" Novo-Dmitrievakain from the Bolsheviks. From April–June 1918, he served as chief of staff to a cavalry brigade commanded by General Viktor Pokrovsky active in southern Russia. On 27 June 1918, he took command of the 1st Kuban Mounted Regiment, and on 14 August 1918 he was promoted to take command of the 1st Mounted Brigade. On 19 November 1918, he assumed command of the 1st Mounted Division. On 8 December 1918, he was promoted to major general.