Following the dissolution of the Soviet Union into its fifteen constituent republics in December 1991, the aircraft and personnel of the Soviet Air Forces - the VVS were divided among the newly independent states. General Pyotr Deynekin, the former deputy commander-in-chief of the Soviet Air Forces, became the first commander of the new organisation on 24 August 1991. Russia received the majority of the most modern fighters and 65% of the manpower. The major commands of the former Soviet VVS - the Long Range Aviation, Military Transport Aviation and Frontal Aviation were renamed, with few changes, Russian VVS commands. However, many regiments, aircraft, and personnel were claimed by the republics they were based in, forming the core of the new republics' air forces. Some aircraft in Belarus and Ukraine (such as Tu-160s) were returned to Russia, sometimes in return for debt reductions, as well as a long range aviation division based at Dolon in Kazakhstan.

During the 1990s, the financial stringency felt throughout the armed forces made its mark on the Air Forces as well. Pilots and other personnel could sometimes not get their wages for months, and on occasion resorted to desperate measures: four MiG-31 pilots at Yelizovo in the Far East went on hunger strike in 1996 to demand back pay which was several months overdue, and the problem was only resolved by diverting unit monies intended for other tasks. As a result of the cutbacks, infrastructure became degraded as well, and in 1998, 40% of military airfields needed repair. The situation only began to improve after Putin took power and military budgets were greatly increased.

The VVS participated in the First Chechen War (1994–1996) and the Second Chechen War (1999–2002). These campaigns also presented significant difficulties for the VVS including the terrain, lack of significant fixed targets and insurgents armed with Stinger and Strela-2M surface-to-air missiles.

During the 1990s the Sukhoi design bureau designed a replacement bomber aircraft, the T-60S. This aircraft did not reach the production stage. A further abortive design project was the MiG 1.42.

The former Soviet Air Defence Forces remained independent for several years under Russian control, only merging with the Air Forces in 1998. The decree merging the two forces was issued by President Boris Yeltsin on 16 July 1997. During 1998 altogether 580 units and formations were disbanded, 134 reorganized, and over 600 given a new jurisdiction. The redistribution of forces affected 95% of aircraft, 98% of helicopters, 93% of anti-aircraft missile complexes, 95 % of the equipment of radiotechnical troops, 100% of anti-aircraft missiles and over 60% of aviation armament. More than 600,000 tons of material changed location and 3500 aircraft changed airfields. Military Transport Aviation planes took more than 40,000 families to new residence areas.

The number of servicemen in the Air Force was reduced to about 185 000 from the former combined number of 318,000. 123,500 positions were abolished, including almost 1000 colonel positions. The resignation of 3000 other servicemen included 46 generals of which 15 were colonel generals. On 29 December 1998 Colonel General Anatoly Kornukov, a former Air Defence Forces officer and new commander-in-chief of the merged force, succeeding Deynekin, reported to the Russian defence minister that the task had 'in principle been achieved'. General Kornukov established the new headquarters of the force in Zarya, near Balashikha, 20 km north of the centre of Moscow, in the former PVO central command post, where the CIS common air defence system is directed from.