The long-standing deputy governor will take office on July 8, after the expiry of Zeljko Rohatinski's term.
Eighty-nine MPs voted in favour, while nine from the opposition Croatian Democratic Alliance of Slavonia and Baranja and the Labour Party abstained.
With this vote, parliament wrapped up this week's sitting and will reconvene on Monday.
On the occasion of Vujcic's appointment, the Croatian Banking Association (HUB) said the HNB "has achieved good cooperation with banks because our common goal is the security and stability of the system and we are confident that the constructive cooperation between the HNB and the HUB will continue."