In Febuary 1964 the Czechoslovak Ministry of Defense issued a preliminary technical specification for a new trainer aircraft to replace the L-29. A developement team, headed by the Chief Designer Jan Vlcek and the Chief of Preliminary Design Karel Dlouhy of Aero, had already been looking at a number of perspective replacements. It was necessary then to respect the reccomendations of the "Main Customer" - ie: Soviet Union (who eventually ended up getting over 2/3 of the production!) There was no possibility to manufacture such an aircraft without an obligation about it's future acquistion. Over the next couple of years, military jet trainers became the main topic within the Czechoslovak aviation industry.

It was decided that the prototypes were to be equipped with modified AI-25 turbofans - AI-25's originally powering the Yak-40. The company responsible for the AI-25W modification was Motorlet in Jinonice and VZLU in Letnany were tasked with developing the VS-1 ejection seat. A milestone in the production was the flight of prototype L-39 X-02, flown by Rudolf Duchon from the Aero airfield on 4 November 1968.

The flight tests showed that the L-39 had excellent flight characteristics with the aerodynamically smooth design. Some problems were incounted with the powerplant and engine intakes, which had to be modified, resulting in the cross-section being enlarged. Three prototypes were flown and the next two airframes underwent ground testing. The advanced Enviroment Control System (ECS) was developed and tested, the next protype already with the final design of air intakes was used for testing of an engine starter driven by the Saphir 5 air turbine of French design, thus providing the aircraft with full capability of being independant of ground power sources.

As a final powerplant of the L-39, the AI-25TL turbofan was selected, produced by Progress in the Ukraine, which became the exclusive engine supplier. In 1971 the AI-25TL was tested on the second and seventh prototypes, together with other modifications. In the same year, preperation was made for the series production at Aero and the aircraft was officially named "Albatros". The first aircraft of the preproduction (zero) series were handed over to the Czechoslovak Airforce on 28 March 1972.

Extensive testing continued along side the beginning of series production, resulting in some systems modifications. The L-39 X-07 prototype completed the next phase of military and contractor tests by the summer of '72, and a year later it passed State Verification tests in the Soviet Union, therefore complying with the requirements for deployment to Soviet military academies.

As the new versions of "Thirty Nines" began to appear in 1977, the basic version was retitled L-39C. It is equipped with mostly equipment of Soviet origin.