South America underwent a span of isolation in the Cenozoic, during which an endemic fauna developed, including a diverse group of native ungulates. Among them, Proterotheriidae (Litopterna, Pan-Perissodactyla) were small to medium-sized hoofed herbivores mainly documented from the Oligocene to the Pleistocene. The study of proterotheriid mammals, specifically their cranial morphology, has been challenging due to the limited availability of materials, leading to a heavy reliance on dental evidence in their descriptions. This issue is particularly evident for late Neogene records, where comprehensive cranial studies have been lacking. Herein, we study a juvenile proterotheriid individual referred to Neobrachytherium intermedium recovered from Early Pliocene outcrops of northwestern Argentina. Our research focuses on cranial morphology, particularly on the dorsal and orbitotemporal regions, mesocranium, and basicranial structures. By employing noninvasive techniques, we describe the petrosal anatomy and compare it in a broader phylogenetic context. We also provide insights into ontogenetic stages within the genus. We find singular arrangements and structures for the genus (e.g., tuberosities in the postglenoid process) as well as traits shared with other mammals that are distinct from those found in other SANUs and pan-perissodactyls, such as Notoungulata (e.g., ringlike ectotympanic, gracile tympanohyal, poorly developed epitympanic wing and medial flange, large hiatus Fallopii). Traits such as the position and shape of the m. tensor tympani fossa and the development of the jugular notch may be synapomorphies of Litopterna, but this cannot be determined without resolving the phylogenetic position of Indalecia grandensis, which has been suggested to be a basal Litopterna. Considering ontogenetic observations, features like the frontal sulcus, the supraorbital foramen, and the palate configuration exhibit age-related changes. The occlusal patterns of teeth undergo substantial changes with wear, affecting loph morphology. Variations in deciduous premolars are observed within the same individual. These findings emphasize the importance of considering ontogenetic and individual variations when analyzing cranial and dental remains for taxonomic and phylogenetic purposes. The study provides valuable information for understanding late Neogene proterotheriids and the broader context of cranial evolution within Litopterna, highlighting the necessity for more comprehensive research.