During the Russian Civil War, Malyshev joined the Red Army in March 1919 and was sent to the 7th Rifle Division, with which he served as chief of the machine gun detachment of the 30th and 58th Rifle Regiments. The division was sent to the Eastern Front with the 2nd Army, fighting against the forces of Kolchak in battles in the Votkinsk area and in the capture of Votkinsk and Izhevsk. In the summer of 1919 the division was sent to the Southern Front, where it fought in battles against the Armed Forces of South Russia in the area of Oboyan and Sudzha. In the fall the division fought in the Orel–Kursk operation and the capture of Dmitrovsk, and in January 1920 in the suppression of anti-Soviet resistance in the area of Glukhov, Putivyl, and Konotop. In April Malyshev was appointed assistant commander for personnel of the 58th Rifle Regiment, fighting in the Polish–Soviet War on the Western Front, then in the suppression of the forces of Stanisław Bułak-Bałachowicz in the area of Ovruch and the Makhnovists in Poltava Governorate. For distinguishing himself in battle, Malyshev was awarded the Order of the Red Banner in May 1920.