We report a new, small-sized atoposaurid crocodyliform from the Upper Jurassic of Langenberg, Northeastern Germany. Atoposaurids are small-sized Mesozoic crocodyliforms of mainly European distribution, which are considered to be phylogenetically close to the origin of Eusuchia. Knoetschkesuchus langenbergensis gen. nov. sp. nov. is represented by two well-preserved skulls and additional cranial and postcranial remains representing different ontogenetic stages. 3D reconstructions of a juvenile skull based on micro-computed tomography allow the most detailed description of cranial remains of any atoposaurid hitherto presented. Our new analysis contradicts previous preliminary assignment of the Langenberg atoposaurids to Theriosuchus. Knoetschkesuchus gen. nov. is characterized in particular by the presence of two dental morphotypes in the maxilla and dentary, slit-like secondary choanae within a narrow groove on the surface of the pterygoid, absence of lacrimonasal contact, presence of an antorbital foramen and an external mandibular fenestra, and proportional characters of the interorbital and intertemporal region. A similar combination of characters allows attribution of Theriosuchus guimarotae to Knoetschkesuchus, forming the new combination Knoetschkesuchus guimarotae. Our analysis provides an osteological basis for the separation of Theriosuchus and Knoetschkesuchus and helps further delineate generic differences in other closely related crocodylomorphs. Our phylogenetic analysis corroborates inclusion of Knoetschkesuchus into Atoposauridae and supports a position of Atoposauridae within Eusuchia.