Whitley's boxfish was first formally described in 1931 by the American zoologist Henry Weed Fowler with its type locality given as the Marquesas Islands.

Fowler's name was a replaced ment for Ostracion ornatus proposed for this species by Henri Hollard in 1857 which was preoccuppied by Ostracion (Aracana) ornata, a species described by John Edward Gray in 1838.

[4] Whitley's boxfish is classified in the genus Ostracion, this name means "little box" and is an allusion to the shape of the body of its type species, O. cubicum.

The specific name honours the British-born Australian ichthyologist Gilbert Percy Whitley, Whitley drew Fowler's attention to the fact that Hollard's name needed to be replaced.

It is found at depths between 3 and 27 m (9.8 and 88.6 ft) in clear lagoons and seaward reefs.