Abstract The monotypic scombrid fish Micrornatus is represented by a single skull from the early Eocene (Ypresian) London Clay Formation of southeastern England. Although Arthur Smith Woodward substantially increased the diversity of scombrids and scombrid-like taxa known from this deposit, he seems not to have studied the fossil that would later be recognized as Micrornatus . Here we re-examine this specimen using computed microtomography, with two principal aims: first, a revised anatomical account with an emphasis on concealed features; and, second, ‘proof-of-concept’ for the tomographic study of fish crania from the London Clay. Scans reveal new details of the braincase, suspensorium and ventral hyoid arch. We compare the cranial anatomy of Micrornatus with other members of Eocoelopomini, a group also containing the genera Eocoelopoma , Palaeothunnus and possibly Landanichthys . Clarification of the taxonomy and phylogeny of early fossil scombrids is needed, and we suggest that computed tomography will be a useful tool for revealing the anatomical evidence needed to accomplish this goal. Supplementary material: Micrornatus hopwoodi NHMUK PV OR 36136 PLY files are available at: http://doi.org/10.6084/m9.figshare.1561381