A graduate of the Paul Military School (1910), Pepelyayev took part in World War I in the rank of lieutenant colonel and distinguished himself at Przasnysz and Soldau. After the Russian Revolution, he took the helm of the White movement in his native Siberian city of Tomsk, joining forces with the White Czechs.
In summer 1918 Pepelyayev's corps was involved in a remarkable expedition to the east along the Trans-Siberian Railway. It was as a consequence of this expedition that the Whites managed to bring Siberia under their direct control. On 18 June Pepelyayev entered Krasnoyarsk; on 26 August he advanced as far east as Chita. Having crossed Transbaikalia, Pepelyayev's forces linked up with the Amur Cossacks of Grigory Semyonov in early September.
In December, Pepelyayev's forces resumed their high tempo advance, this time to the west. His greatest victory was the capture of Perm, where about 20,000 Red Army soldiers were taken prisoner on 24 December 1918. Further advance on Vyatka was impeded by heavy frost. As the spring rasputitsa arrived Pepelyayev's position deteriorated. His armies had outrun their supply lines and were exhausted from many months of incessant warfare, while the Red Army was pouring newly raised troops into the area.
Pepelyayev's taking of Glazov on 2 June 1919 was his last signal success. During the following months, his First Siberian Army suffered a series of setbacks and fell back on Tobolsk, where they were forced to make a last stand against the Bolsheviks. By the end of the year, the White Army had collapsed in panic and abandoned Omsk, followed by Tomsk.
Pepelyayev's smouldering conflict with Kolchak came to a head in mid-December when he issued threats to arrest the White admiral. They were reconciled by Viktor Pepelyayev before Anatoly was disabled by typhus and transferred for convalescence to Harbin. The remains of his army joined that of Vladimir Kappel and crossed the frozen Lake Baikal during the Great Siberian Ice March.
During his stint in Harbin, the former general was employed in menial jobs, including those of carpenter and taxi driver. Still, he harboured the intention of wresting Siberia from the Bolsheviks. On 31 August 1922 Pepelyayev and 553-strong volunteer "druzhina" embarked on the last major operation of the Civil War. They sailed into the Sea of Okhotsk and disembarked at the port of Okhotsk, aiming to penetrate westward into the rugged mountainous country.
In September Pepelyayev sailed up the Okhota River into Siberia, with his eyes set on Yakutsk. His troops swarmed over Yakutia, but were contained by Ivan Strod's Bolsheviks. Numerically weaker, they were defeated by sheer weight of numbers. After abandoning the key settlement of Amga, Pepelyayev pressed on towards the Pacific in the hope of making a crossing to Sakhalin. This final campaign saw him defeated near Okhotsk on 1–2 May. Pepelyayev surrendered to the Bolsheviks after the siege of the seaside village of Ayan on 17 June 1923. This was the last siege of the Russian Civil War.
Lieutenant General Pepelyayev was tried by the Vladivostok military tribunal and sentenced to execution by firing squad. After he asked Mikhail Kalinin for pardon, the sentence was commuted to ten years in prison. He served this term in the Yaroslavl prison, then in Butyrki. Pepelyayev was finally set at liberty on 6 June 1936 and was employed as a carpenter in Voronezh. In August 1937, during The Great Purges, he was again arrested, taken to Novosibirsk, tried on charges of having created a counter-revolutionary organization, sentenced to death and executed on 14 January 1938 alongside Ivan Strod as 'enemies of the people'. Pepelyayev was posthumously cleared of these charges and rehabilitated in 1989.Order of St. Anna, 4th class with the inscription "For Bravery", 3rd class and 2nd class
Order of St. Stanislaus, 3rd and 2nd classes
Order of St. Vladimir, 4th class, with swords and bow
Order of St. George, 4th class (27 January 1917)
Gold Sword for Bravery (27 September 1916)