The Pannonian basin together with the surrounding orogenic belts of Alps, Carpathians, and Dinarides represents a geologically complex region that exhibits significant lateral variation in lithospheric structure. Accurate earthquake locations are a prerequisite for better understanding of neotectonic activity driven by the movement of the Adriatic microplate and to facilitate seismic hazard studies. We relocate the seismicity recorded in the digital instrumental period between 1996 and 2016 using the state‐of‐the‐art iLoc location algorithm. The relative abundance of ground‐truth (GT) events allows us to evaluate the performance of the 1D local velocity models used in the past and the global 3D upper‐mantle and crustal regional seismic travel time (RSTT) velocity models. We demonstrate that the 3D velocity model captures the major 3D velocity heterogeneities and provides an improved view of the seismicity in the region.