The species distribution of Eastern School Whiting (Sillago flindersi), spans more than 15 degrees latitude along the southeastern Australian coastline. It is targeted extensively by commercial trawl fisheries and catches and management are shared across several jurisdictions. To improve spatial allocation of cross-jurisdictional stock assessments and harvest strategies, we investigated the stock structure of S. flindersi sampled from 16 locations across the species’ distribution using otolith chemistry. Trace element profiles were measured from the juvenile core to outer adult edge of sagittal otolith thin sections using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). Trace element profiles were aligned with the underlying growth increment microstructure to investigate variations in otolith chemistry across the lifetime of each fish and among locations. Significant ontogenetic and geographical variation in chemical composition of otoliths was detected, particularly among fish from locations at the extremities of the species’ distribution. However, evidence for considerable overlap and mixing of S. flindersi populations across adjacent locations was also found. The results were consistent with recent genetic data from next-generation sequencing that detected only weak isolation by distance for samples from South Australia and Tasmania, and indicated panmixia and a single biological stock for stock assessments and management.