The Eastern school whiting was long thought to be synonymous with the closely related species "Sillago bassensis", the southern school whiting, with this relationship first applied in 1892 by Cohen. It took until 1985 before McKay identified two distinct forms of "Sillago bassensis", which he believed to subspecies, thus erecting "Sillago bassensis flindersi" for the eastern subspecies and "Sillago bassensis bassensis" for the western subspecies. These subspecies were formally promoted to separate species status in 1992, during a second review of the family by McKay after the two species were found to occur sympatrically in Bass Strait. The binomial name of the species was named in honour of the explorer Captain Matthew Flinders, who circumnavigated and extensively mapped the coastline of Australia.