Fossil remains of Eosipterus dated back to the Aptian stage of the Early Cretaceous, 125 million years ago.

The genus is based on the holotype specimen, GMV2117, found near Jinggangshan in western Liaoning Province, in the Yixian Formation.

The wing finger has the standard four phalanges, a difference from the possibly related Beipiaopterus which has lost the fourth phalanx.

The authors placed Eosipterus in a general Pterodactyloidea incertae sedis; in 1999 a placement within Pterodactylidae was suggested, and even a synonymy with Pterodactylus was proposed within a hypothesis that the lower Yixian Formation dated from the Late Jurassic.

In the analysis, they recovered Eosipterus within the family Ctenochasmatidae, more precisely within the tribe Pterodaustrini, placed in a more derived position than Pterodaustro.