Trionychid (softshell) turtles have a peculiar bauplan, which includes shell reductions and cranial elongation. Despite a rich fossil record dating back to the Early Cretaceous, the evolutionary origin of the trionychid bauplan is poorly understood, as even old fossils show great anatomical similarities to extant species. Documenting structural detail of fossil trionychids may help resolve the evolutionary history of the group. Here, we study the cranial and mandibular anatomy of Plastomenus thomasii using µCT scanning. Plastomenus thomasii belongs to the Plastomenidae, a long-lived (Santonian–Eocene) clade with uncertain affinities among trionychid subclades. The skulls of known plastomenids are characterized by unusual features otherwise not known among trionychids, such as extremely elongated, spatulate mandibular symphyses. We use anatomical observations for updated phylogenetic analyses using both parsimony and Bayesian methods. There is strong support across methods for stem-cyclanorbine affinities for plastomenids. The inclusion of stratigraphic data in our Bayesian analysis indicates that a range of Cretaceous Asian fossils including Perochelys lamadongensis may be stem-trionychids, suggesting that many features of trionychid anatomy evolved prior to the appearance of the crown group. Divergence time estimates from Bayesian tip-dating for the origin of crown Trionychia (134.0 Ma) and Pan-Trionychidae (123.8 Ma) constrain the evolutionary time span during which the trionychid bauplan has evolved to a range of < 11 million years. Bayesian rate estimation implies high morphological rates during early softshell turtle evolution. If correct, plastomenids partially fill the stratigraphic gap which results from shallow divergence times of crown cyclanorbines during the late Eocene.