The clinical diagnosis and treatment of autoimmune epilepsy have long been confronted with the coexistence of overdiagnosis and underdiagnosis, and this dilemma is particularly challenging in clinical teaching. Through a retrospective analysis of two typical cases, this article analyzes in depth the underlying reasons from a teaching perspective, summarizing them into three aspects: lag in updating the conceptual framework, biased interpretation of ancillary test results, and rigid diagnostic pathways caused by cognitive biases. Accordingly, this article proposes four targeted teaching strategies—reverse teaching method, structured assessment framework, simulated clinical decision-making training, and multidisciplinary collaborative discussions—aiming to systematically enhance learners' comprehensive judgment abilities. The focus of teaching should thereby shift toward cultivating students' reasoning skills in dealing with clinical uncertainty, and through structured reflection on typical cases, forging evidence-driven critical thinking, ultimately achieving a fundamental transformation from knowledge transmission to thinking training.