The MiG-21 jet was originally taken to Austria by pilot Rudolf Peresin, who refused to bomb his native Croatia in the war for independence.
It is due to be displayed in front of the defence ministry in Zagreb later this month.
Croatian army chief of staff General Drago Matanovic said the plane was “a symbol of the heroism in the war for the homeland”, the Hina news agency reported.
Yugoslavia fell apart in a series of bloody wars in the 1990s in Croatia, Bosnia and Kosovo, that left more than 130,000 people dead and millions displaced.
Croatia declared independence from the former Yugoslavia in 1991, sparking one of the first of the conflicts.
Peresin explained his decision at the time of his defection: “I am Croat and I do not want to shoot on Croats.”
He was killed in May 1995 at the end of the bloodshed between Croatia and the Belgrade-backed ethnic Serb minority. The war claimed 20,000 lives.
The jet will be displayed at the Zagreb defence ministry on May 12th to mark the 24th anniversary of the pilot's death.
It will then be stored in a military airport close to Zagreb, awaiting installation in a future Croatian military museum.