Trace fossils preserved in fossilized tissues provide a key resource for exploring the paleoecology of past ecosystems. Endobiont organisms are commonplace in modern ecosystems, but their trace fossils on vertebrates are rare as the organisms usually attack or attach to soft tissue. Here, we report the novel occurrence of flask-shaped boreholes representing the ichnotaxon Karethraichnus n. isp. in the carapace of the basal leatherback sea turtle Mesodermochelys sp. from the Upper Cretaceous of northern Japan. The distribution of the boreholes was determined by observing the carapace surface. Using X-ray computed tomography, we were also able to produce a 3D reconstruction of the whole carapace and examine a cross section of a borehole to analyze the histological aspects of the bone. In total, 43 holes were observed, 12 holes contained probable pholadoid bivalves, and 32 holes were not bored entirely through the carapace. Some of the bivalves found in the holes are larger than the aperture of the hole, suggesting that they continued to grow during boring. The holes are hemispherical to clavate in shape and developed on the exterior side of the carapace. Healing traces, i.e., repairing of bone, can be observed at the surface of the holes. Our observations strongly suggest that these pits were bored by pholadoid bivalves while the turtle was alive. This is the first report of the behavior of boring bivalves as sea-turtle endobionts boring into a unique free-living, i.e., “swimming substrate”.