The stem turtle Eileanchelys waldmani is known from the Bathonian deposits of the Kilmaluag Formation, Isle of Skye, Scotland. A description of all the currently available material, including several skulls and shells, is provided herein. Eileanchelys waldmani is characterised by a mosaic of plesiomorphic and derived features. The former include a flat vomer, a reduced posterior extension of the pterygoid, the absence of flooring of the cavum acustico-jugulare, the absence of proper recessus scalae tympani, wide vertebral scales, a vertebral 3–4 sulcus on neural 6, a pair of mesoplastra meeting medially, and platycoelous cervical vertebrae. Derived features include a prefrontal–vomer contact, an elongate postorbital skull, a well-developed antrum postoticum, and a slender processus interfenestralis of the opisthotic. Eileanchelys waldmani also possesses unique features such as a possible ninth neural or supernumerary suprapygal of unusual shape, as well as a broad first suprapygal that contacts the peripherals laterally. Additionally, E. waldmani documents the evolution of the vomer and basicranium from basalmost turtles to the crown-group.