In 1990, after the first democratic elections held in Croatia, Zagal changed its name in July 23 to its current identification of Croatia Airlines.
In 1991 the airline signed an agreement with Adria Airways and then was able to lease a McDonell Douglas MD-82 to start domestic jet services. That year also saw the airline's first international route when a flight was inaugurated from Zagreb to Split in Yugoslavia.
1992 was a tough year for the company, because it had to stop flying momentarily because of the Croatian conflict. However, as soon as flights were re-commenced, Croatia Airlines bought three Boeing 737's from Lufthansa. They also became a member of the IATA, or International Air Transport Association.
1993 saw two ATR-42's and two more 737's join the fleet, and many offices get opened in several European cities. The company bought over a travel agency, Ozbor, to organize travel for groups and individuals.
By 1994, Croatia Airlines had welcomed it's one millionth passenger on a plane. Later that year, Pope John Paul II flew the airline on a trip to Croatia.
In 1995, another ATR-42 was welcomed, as was the two millionth passenger. And in 1996, Croatia Airlines became the first airline to fly to Sarajevo.
1997 saw the airline's first Airbus A320 arrive. It was nicknamed Rijeka. In 1998, another first plane of a new type arrived when the airline's first Airbus A319 joined the fleet. This plane was nicknamed Zadar. Also that year, Croatia Airlines became a member of the AEA or Association of European Airlines.
By 1999, two more Airbus jets had arrived and Croatia Airlines started selling their Boeing part of the fleet. Another important event occurred when the airline flew it's five millionth passenger.
In 2000 two more Airbus planes arrived and an Automated Ticketing System inaugurated.
2001 saw Croatia Airlines get maintenance and technical performing certificates from a German aviation authority named LBA