Mario Barlovic, 52, was convicted by the Zagreb Court for Minors after a five-month trial for "forcible sexual intercourse with a disabled child in a particularly humiliating manner" in 1998-1999, the state-run news agency HINA reported.
Barlovic was arrested a year ago, when the state prosecution reopened the case after local media published for the first time a 2002 government report suggesting abuses in the orphanage run by the Catholic charity Caritas. It cares for about 150 children in the village of Brezovica, outside Zagreb.
The case had been dropped at the time, but the new investigation last year revealed more alleged cases of abuse of orphans there. A former orphanage cook was subsequently also arrested and charged with sexual abuse and the ex-head of the institution, Jelena Brajsa, is also being tried separately on charges of covering up the crimes of her employees, the AP reports.
Brajsa who for decades was hailed in Croatia for her care for orphans insists she knew nothing about the wrongdoing in the orphanage. The church removed her from the orphanage following the affair.
The case shocked Croatia, where nearly 90 percent of people are Roman Catholics and where the church, and Caritas, enjoy wide respect. Many in Croatia believe the case was covered up for years because authorities hesitated to go up against the influential Catholic church.