Apatemys is a member of the family Apatemyidae, an extinct group of small and insectivorous placental mammals that lived in the Paleogene of North America, India, and Europe.

Apatemyids are scarce even in the faunas where they are most often discovered, and constructing valid taxonomy is challenging since the specimens are typically retrieved in small sample sizes.

Apatemys has 14 sister taxa also belonging to the family Apatemyidae, including Apatemyinae, Asiapator, Carcinella, Eochiromys, Frugivastodon, Heterohyus, Jepsenella, Labidolemur, Russellmyinae, Russellmys, Sinclairella, Stehlinella, Teilhardella, Unuchinia, and Unuchiniinae.

[5] The species of the genus Apatemys belong to the suborder Apatotheria, whose sister taxa are Didelphodonta, Cimolestidae, Palaeoryctida, Pantodonta, Pantolesta, Pentacodontidae, Sarcodontidae and Todralestidae.

[6] Apatemyids are highly specialized eutherian mammals prevalent throughout Tertiary deposits of North America, Europe, India and Mongolia.

The elongated digits II and III allowed apatemyids to reach within the tiny crevices of tree bark and extract the larvae to feed on.