Later in 1991, Croatia Airlines signed an agreement with Adria Airways which allowed it to lease a McDonnell Douglas MD-82 to commence domestic jet services between Zagreb and Split.

Croatia Airlines acquired three Boeing 737s from Lufthansa and became a member of the International Air Transport Association (IATA).

As the flag carrier of newly independent Croatia, the airline launched its first international service on 5 April 1992, from Zagreb to Frankfurt.

[8][9] Losses have been made for several years; in November 2012, the government announced that it would provide HRK 800m ($ 136m) for Croatia Airlines to become cost-effective from 2013 on.

The government is seeking to restructure the airline, which includes plans to cut its workforce by ten percent within two years and it is also looking for a strategic investor.

[10] In February 2020, Croatia Airlines announced two new seasonal flights to Podgorica and Sofia operated by Bombardier Dash 8 Q400.

[12] In October 2022, Croatia Airlines announced plans to reduce their fleet and replace all current aircraft with six new Airbus A220-300 by 2026.

[15] In September 2023, Croatia Airlines sold and leased back its entire Airbus fleet from lessor World Star Aviation.