Research on neurodevelopmental disorders (NDDs) has led us to refine our theoretical and methodological approaches. We explore whether new deficit clusters in line with the Research Domain Criteria, a novel multifactorial framework, optimally explain known conditions such as ADHD, DLD, or SLD in reading. Following the PRISMA guidelines for systematic reviews, we assimilated relevant literature from 2015 to 2025 on the RDoC framework and the above conditions. We retrieved 3486 studies focusing on the RDoC Cognitive Systems domain from databases, including PubMed, PsycINFO, and Web of Science. Studies were processed with the RayYan software. Fifteen studies met all inclusion criteria. Findings show that RDoC-informed neural and cognitive phenotypes were only partially aligned with DSM-based diagnoses. Moreover, deficits in Cognitive Control and Working Memory cut across known diagnoses, thus serving as transdiagnostic markers. The RDoC framework helps distinguish the neural, cognitive, linguistic, and behavioral deficits that cut across NDDs.