Epilepsy is an important or common clinical manifestation of numerous rare diseases, frequently emerging as an initial or core symptom in children and adolescents. Due to the low prevalence and heterogeneous clinical presentations of rare diseases, as well as generally insufficient awareness and limited research among both patients and healthcare providers, epilepsy-related rare diseases are often subject to diagnostic delays, misdiagnosis, and suboptimal management in routine clinical practice. To address these challenges, the development of a systematic, clear, and clinically applicable classification catalogue for epilepsy-related rare diseases is critical for enhancing disease recognition, standardizing diagnostic and therapeutic methods, developing expert consensus, and optimizing healthcare resources allocation. Focusing on the prominent challenges of epilepsy in rare diseases, this article systematically outlines the background, classification principles, and overall framework for epilepsy-related rare diseases. Furthermore, we further highlight the pivotal role of this classification system in improving clinical management, promoting multidisciplinary collaboration, and guiding health policy formulation. The proposed framework is intended to serve as a foundational reference for the standardized and holistic management of epilepsy-related rare diseases.