In the spring of 2008, a number of Georgian drones were shot down by Abkhazian separatist forces over the Abkhazia region. The Abkhazian separatist forces claimed that one of its missile-equipped L-39s had shot down a Georgian Hermes 450 unmanned reconnaissance drone.
The Taliban air force managed to obtain some five L-39C from the former communist government air force remnants and press some, with foreign help and pilots, into combat during the later part of the 1996-2001 phase of the Afghan civil war against the Northern Alliance. In early 2001, only two were operational
L-39s, along with older L-29s, were used extensively in ground attack missions by Azeri forces in the Nagorno-Karabakh War. Several were shot down by Nagorno-Karabakh Defense Army air defences.
The newly de facto independent Chechen Republic of Ichkeria found itself with dozens of L-39s (as well as several L-29s, three MiG-17s, two MiG-15UTIs, helicopters and other transport and civilian aircraft) left at Khankala and Kalinovskaya airbases by the Soviet Air Force in 1992. Most of these, however, were reportedly abandoned or not in flyable condition, but during the August–November 1994 conflict between nationalist and pro-Russian forces L-39s were deployed and were possibly one of the few air attack (and possibly recce) elements on Dzhokar Dudayev's forces. At least one was reported as shot-down near Goragorsk on October 4 by a Strela-2 MANPADS fired by Doku Zavgayev's pro-Russian militia. The pilot, Col. Ali Musayev and the co-pilot Dedal Dadayev were killed.
One of the main reasons that prompted the first Su-25 air raids that destroyed the Chechen air force on the ground, and started the Russian intervention, were Dudayev's air force preparations (spotted by recce Su-24MRs) and fears that his aircraft could slow or deter the Russian air and ground campaign, as well as the capability of several aircraft to conduct kamikaze attacks on Russian nuclear or power plants (specially by means of the ejection seat in most aircraft, notably the L-39, by stuffing them up with explosives and converting them into improvised cruise missiles).
Libya acquired some 180 L-39ZOs around 1978 which served at Sabha and Okba Ben Nafi flying schools along with Yugoslav-made G-2 Galeb for advanced jet training and Italian-made SF.260s (for primary training).
The L-39s were deployed during the Chadian-Libyan conflict, mainly to Ouadi Doum air base. During the final Chadian offensive in March 1987, the Chadians captured Ouadi Doum along with several aircraft (11 L-39s included) and Soviet SAM systems and tanks. A Chadian report to the UN, reported the aforementioned capture on 11 L-39s and the destruction (or downing) of at least four of them.
In the midst of that conflict, on April 21, 1983 three LARAF Il-76TDs and one C-130 landed at Manaus Airport, Brazil after one of the Il-76s developed some technical problems while crossing the Atlantic Ocean. The aircraft were then searched by the Brazilian authorities: instead of medical supplies – as quoted in the transport documentation – the crate of the first of 17 L-39s bound for Nicaragua together with arms and parachutes, to support the country's war against US-backed Contras were found. The cargo was impounded for some time before being returned to Libya, while the transports were permitted to return to their country.
The Syrian Arab Air Force has a number of armed L-39ZA light attack variants. Since 2012, during the Syrian civil war, L-39s have been routinely deployed against rebel ground forces and a number of aircraft have been shot down by ground fire. They were first used operationally during the Battle of Aleppo, striking rebel-held positions.
Insurgents captured L-39s along with their support equipment after raiding the Al-Jarrah base in February 2013, though it is uncertain if the planes are airworthy.
In October 2014 insurgents destroyed at least one L-39 on the ground at Nayrab Airbase using a TOW missile.
While newer versions are now replacing older L-39s in service, thousands remain in active service as trainers, and many are finding new homes with private warbird owners all over the world. This is particularly evident in the United States, where their $200,000–$300,000 price puts them in range of moderately wealthy pilots looking for a fast, agile personal jet. Their popularity led to a purely L-39 Jet class at the Reno Air Races, though it has since been expanded to include other, similar aircraft.
In September 2012 there were 255 L-39s registered with the US Federal Aviation Administration and four registered with Transport Canada. Several display teams use the L-39 such as the Patriots Jet Team (6 L-39s), the Breitling Jet Team (7 L-39s) and the Black Diamond Jet Team (5 L-39s).
There are also several L-39 available for private jet rides in Czech Republic, France, Germany, Spain and the USA. These L-39s are mostly in private hands, but some also belong to government agencies, such as those in Vyazma, Russia.