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Pukanić was born in Zagreb. He graduated from the Faculty of Political Sciences of the University of Zagreb. He had worked since 1991 as an editor of the popular weekly Globus. In 1995 he founded Nacional and stayed there as the editor-in-chief until 2000. The same year Pukanić received an award from Croatian Journalists' Association. He also later received an award for a 2003 interview with army general Ante Gotovina, who was at the time on the run due to accusations of war crimes by the ICTY.

Pukanić had a wife, Mirjana, and a daughter, Sara.

Pukanić was assassinated around 6.20 p.m. by a bomb planted in the trashcan next to his parked Lexus on October 23, 2008 in the center of Zagreb, the capital of Croatia. He was killed alongside Niko Franjić, the Nacional marketing manager. The incident happened on Stara Vlaška Street, only two street blocks east of the main Zagreb square, Ban Jelačić Square.

Nacional reporter Plamenko Cvitić was the first news reporter on the scene. The police immediately blocked the traffic around the site of assassination, causing immense traffic jams all over the city center. Prime Minister Ivo Sanader declined a proposal for entering a state of emergency