The 16th Army Headquarters was formed in July 1940 in the Transbaikal Military District to command Soviet forces deployed in the Dauriya area.

On 25 May 1941, four weeks before the commencement of the German invasion of the Soviet Union, Operation Barbarossa, the army received orders to deploy (with six Trans-Baikalian divisions) to Ukraine to be subordinated to the Kiev Special Military District.

Soon after the commencement of Operation Barbarossa a crisis situation developed on the Western Front sector of the frontline, and on 26 June 1941 16th Army was ordered to redeploy to the area of Orsha - Smolensk.

[citation needed] On 20 July 129th Rifle Division's four committed battalions lost 40% of their strength defending the suburbs of Smolensk.

Three days later, a Western Front situation report said that '..during the course of 22.7, 16th Army units, continued to conduct severe street battle to secure Smolensk.

In September 1941 the newly promoted Lieutenant-General Rokossovsky was tasked with defending the Volokolamsk Highway, and preventing any advance by German forces towards Moscow.

[citation needed] 16th Army was formed for the third time on 10 July 1943 in the Far Eastern Front and was based on the Special Rifle Corps.

From the spring of 1945 the Army was responsible for the defense of the Soviet state border with Japan on the island of Sakhalin, and also along the mainland coast of the Tatar Strait from Sovetskaya Gavan to Nikolaevsk-on-Amur.