Unlike the leaders of the Yaroslavl Uprising, representatives of the Soviet power had a completely different understanding of acceptable methods of warfare. After the initial shock from the unexpected uprising, they began a brutal suppression. The Bolsheviks brought in heavy artillery and started shelling the city with incendiary shells, while air bombardments began simultaneously. Three armored trains were used for the suppression. The Red commanders planned to use choking gas, but due to strong winds and rain, this became impossible. Yaroslavl became the first city destroyed by aviation.

A special provincial military-revolutionary committee was created to suppress the uprising, led by the communist Babich, with assistants Guzarsky and Gekker, who commanded on different banks of the river. Interestingly, throughout the fighting, they constantly demanded that the command send new mercenary units of Chinese and Latvians, as the other Red Army soldiers fought poorly, mainly engaging in looting and being difficult to control. The leaders of the suppression also requested 10,000 shells, in addition to those already available.

The rebels held out for about two weeks, their numbers, according to various sources, ranged from 1,500 to 6,000 people, but they were doomed. The allies postponed the landing, and uprisings in other cities were suppressed. Perkhurov suggested breaking through the Red forces and heading to Vologda or Kazan, but the local rebels led by General Karpov refused. In the end, it was decided to send Perkhurov with a small detachment for reinforcements, while the Yaroslavl residents remained to fight. Soon they ran out of ammunition and decided to surrender to a German mission that was engaged in sending German prisoners of war back home. Initially, the mission declared the surrendering individuals as their prisoners, but then deceitfully handed them over to the Bolsheviks.

During the fighting, Yaroslavl suffered significant damage: 20 factories and plants were destroyed, more than 2,000 houses, including 67 government buildings, dozens of churches, and the Demidov Law Lyceum with its unique library. After the fighting ended, the Soviet authorities carried out a mass purge, during which, according to official data, more than 5,000 people were killed, sparing no one. The leader of the uprising, Perkhurov, managed to reach the Volunteer Army, fought in units under the command of Kappel and Kolchak. On the Lena River, he was captured and went through concentration camps in Irkutsk, Chelyabinsk, and Yekaterinburg. He managed to conceal his role in the Yaroslavl Uprising. In January 1921, he was released and appointed as a teacher at the junior command school at the headquarters of the 69th Rifle Brigade. Five months later, his involvement in the anti-Bolshevik rebellion was revealed, Perkhurov was arrested, sent to Moscow, and executed in 1922.

Currently, there is a rethinking of what happened, new books are being published that expose the Soviet lies about the uprising, and a feature film was made for the 100th anniversary.