[2] Fossils of Avitomyrmex, along with other extinct Myrmeciinae ants were first studied and described by Bruce Archibald, Stefan Cover and Corrie Moreau of the Museum of Comparative Zoology in Cambridge, Massachusetts.

[3] Archibald and colleagues originally classified Avitomyrmex as incertae sedis (Latin for "of uncertain placement") within the ant subfamily Myrmeciinae, as the specimens are unable to be properly identified.

[5] In 2008, however, Cesare Baroni Urbani of the University of Basel, Switzerland, noted that no specimen in this genus allows a proper examination of the apomorphy (key diagnostic traits) of the subfamilial or familial characters.

While Baroni Urbani excludes Avitomyrmex from Myrmeciinae and classifies it as incertae sedis in Hymenoptera, the morphological characters and wings show the specimens are undoubtedly a hymenopteran insect.

[6] A 2012 report by Russian palaeoentomologist Gennady M. Dlussky of the Moscow State University describing new Myrmeciinae accepted the classification of Archibald and colleagues without mentioning the comments of Baroni Urbani.

It is suggested that Avitomyrmex may be closely related to other extinct Myrmeciinae ants such as Macabeemyrma and Ypresiomyrma, as well as the extant Nothomyrmecia macrops.

Archibald, Cover, and Moreau coined the specific epithet from the Latin "elongatus" meaning "prolonged" in reference to the elongated morphology of the type specimen.

[11] The holotype specimen is a partial queen which is incomplete, with one forewing and the head fairly preserved, and the other isolated body portions indistinct.

Due to the size of adult workers they cannot be attributed to A. elongatus while the overall petiole, head capsule and mandible structure distinguish it from A. mastax.

The shape of the head was the basis for Archibald, Cover and Moreau choosing the specific epithet systenus, which is from the Greek word systenos meaning "tapering to a point".