Trifunović began his pro career with Crvena zvezda before moving to KK Zadar where he played for 3 seasons under head coaches Dragan Šakota, Slavko Trninić, and Krešimir Ćosić.

He returned to Crvena zvezda in summer 1991, contributing greatly to the club's two back-to-back league titles.

He firmly established his head coaching career in Lithuania with the Lithuanian League club Lietuvos rytas in the years 2006–2008.

However, a loss in the LKF cup and finishing only 3rd in the Baltic League led to Trifunovic parting ways with Rytas in April 2011.

[6] After starting the 2011–12 season without a team, Trifunović shocked everyone when he became the head coach of BC Žalgiris, the archrival of Lietuvos Rytas.

[10] On 9 February 2016, Trifunović was named the head coach of Yeşilgiresun Belediye of the Turkish Basketball Super League.