E. leali was possibly fairly closely related to Avisaurus, another genus of carnivorous enantiornithines, though its exact relationship is unclear. It is placed in a family of its own (Enantiornithidae), though most researchers consider this premature.
Other species from Asia that were previously placed in this genus are now split off. The former Enantiornis martini is now placed in Incolornis, while the former Enantiornis walkeri is now tentatively assigned to Explorornis. The reasons for this are that these birds were described when the diversity of enantiornithine birds was underestimated.