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 Tupolev 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 was felt throughout the armed forces made its mark on the Russian 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 money 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 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.
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 reorganised, 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 3,500 aircraft changed airfields. Military Transport Aviation planes took more than 40,000 families to new residence areas.
The short-lived operational commands were abolished. Two air armies, the 37th Air Army (long-range aviation) and the 61st Air Army (former Military Transport Aviation), were established directly under the Supreme Command. The former frontal aviation and anti-aircraft forces were organised as Air Force Armies and Anti-Aircraft Defense Armies under the military district commanders. There were initially four such armies with headquarters in St.Petersburg (Leningrad Military District), Rostov-on-Don (North Caucasus Military District), Khabarovsk (Far East Military District), and Chita (Siberian Military District). Two military districts had separate Air and Air Defence Corps. When the Transbaikal Military District and Siberian Military District were merged, the 14th Air Army was reactivated to serve as the air force formation in the area.
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 1,000 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 east of the centre of Moscow, in the former PVO central command post, where the CIS common air defence system is directed from.
In 1999 Vladimir Putin became Prime Minister of Russia and then President in 2000; he continued to hold one or the other of these offices through every year since.
In December 2003 the aviation assets of the Russian Ground Forces—mostly helicopters—were transferred to the VVS, following the shooting down of a Mi-26 helicopter in Chechnya on 19 August 2002, that claimed 19 lives. The former Army Aviation was in its previous form intended for the direct support of the Ground Forces, by providing their tactical air support, conducting tactical aerial reconnaissance, transporting airborne troops, providing fire support of their actions, electronic warfare, setting of minefield barriers and other tasks. The former Army Aviation was subsequently managed by the Chief of the Department of Army Aviation.  However, by 2010, it was announced that the 2003 decision to transfer Ground Force Aviation to the Air Force was reversed, with the transfer back to the Ground Forces to occur sometime in 2015 or 2016. 
During the 2000s, the Air Forces continued to suffer from a lack of resources for pilot training. In the 1990s Russian pilots achieved approximately 10% of the flight hours of the United States Air Force. The 2007 edition of the International Institute for Strategic Studies (IISS) Military Balance listed pilots of tactical aviation flying 20–25 hours a year, 61st Air Army pilots (former Military Transport Aviation), 60 hours a year, and Army Aviation under VVS control 55 hours a year. 
In 2007 the Russian Air Force resumed the Soviet-era practice of deploying its strategic bomber aircraft on long-range patrols. This ended a 15-year unilateral suspension due to fuel costs and other economic difficulties after the collapse of the Soviet Union.   Patrols towards the North Pole, the Atlantic and the Pacific Ocean were reinstated, bringing the planes often close to NATO territory, including in one instance flying over the Irish Sea between the United Kingdom and Ireland. 
During the 2008 South Ossetian War, the Russian Air Force suffered losses of between four and seven aircraft due to Georgian anti-aircraft fire. The 2008 Russian military reforms were promptly announced following the war, which according to Western experts were intended to address many inadequacies discovered as a result. The reforms commenced during early 2009, in which air armies were succeeded by commands, and most air regiments becoming air bases.  Aviation Week & Space Technology confirmed that the reorganisation would be completed by December 2009 and would see a 40 percent reduction in aircrew numbers. 
In February 2009, the Russian newspaper Kommersant reported that 200 of the 291 MiG-29s currently in service across all Russian air arms were unsafe and would have to be permanently grounded.  This action would remove from service about a third of Russia's total fighter force, some 650 aircraft. On 5 June 2009, the Chief of the General Staff, Nikolai Makarov said of the Russian Air Force that "They can run bombing missions only in daytime with the sun shining, but they miss their targets anyway".  Maj. Gen. Pavel Androsov said that Russia's long-range bombers would be upgraded in 2009 with the aim of being able to hit within 20 meters of their targets. 
Also in September 2009 it was reported that an East European network of the Joint CIS Air Defense System was to be set up by Russia and Belarus.  This network was intended to protect the airspace of the two countries as defined in the supranational 1999 Union State treaty. Its planned composition was to include five Air Force units, 10 anti-aircraft units, five technical service and support units and one electronic warfare unit. It was to be placed under the command of a Russian or Belarusian Air Force or Air Defence Force senior commander.
In July 2010, Russian jet fighters made the first nonstop flights from European Russia to the Russian Far East.  By August 2010, according to the Commander-in-Chief of the Russian Air Force Aleksandr Zelin, the average flight hours of a pilot in Russian tactical aviation had reached 80 hours a year, while in army aviation and military transport aviation it exceeded 100 hours a year.  On 15 August 2010, the Russian Air Force temporarily grounded its fleet of Su-25 ground attack aircraft to conduct an investigation into a crash that happened during a training mission. The Russian Defence Ministry said that the plane crashed on 6 August 2010, 60 km to the north-west of Step air base in Siberia, according to RIA Novosti .
According to the instructions of the General Staff of the Armed Forces on 1 September 2011, the unmanned aircraft of the Russian Air Force and the personnel operating them moved under the command structure of the Russian Ground Forces. 
As of 2012, the Russian Air Force operated a total of 61 air bases, including 26 air bases with tactical aircraft, of which 14 are equipped with fighter aircraft. In terms of flight hours, pilots in the Western Military District averaged 125 hours over the 2012 training year. Pilots from the Kursk air base achieved an average of 150 hours, with transport aviation averaging 170 hours. 
In February 2014, during the early periods of Russia's annexation of Crimea, the Russian Air Force's assets of the Southern Military District were activated and flown to the peninsula for supporting the rest of the operations. 
On 1 August 2015, the Russian Air Force, along with the Russian Aerospace Defence Forces and the Air Defense Troops, were merged into a new branch of the armed forces, now officially called the Russian Aerospace Forces. 
On 30 September 2015, the Russian Air Force launched a military intervention in Syria, in Syria's Homs region.  On 24 November 2015, during a bombing mission, a Turkish Air Force F-16 shot down a Russian Sukhoi Su-24 that Turkey claimed had violated its airspace.  
In March 2020, the indiscriminate bombing of civilian targets by the Russian Air Force in Syria has been described as "amounting to war crime" by UN HRC report. 
On 9 November 2020, a Russian Mil Mi-24 attack helicopter was shot down mistakenly by the Azerbaijani Armed Forces during the 2020 Nagorno-Karabakh war killing 2 crew members and injuring 1 more. Days later, after the signing of the ceasefire agreement, Russian peacekeepers were deployed to Nagorno-Karabakh with aviation for patrolling its borders. 
Modernisation plans and programs carried out since the 2010s are being continued into 2021 as a part of Russia's State Armament Program for 2018–2027.