Background: Seronegative autoimmune encephalitis (SAE) in children is associated with cognitive deficits, particularly executive dysfunction. However, the relationship between cognitive impairment, disease severity, and lesion burden remains unclear. Identifying these associations could improve patient management and outcomes. This study characterizes neuropsychological symptoms in pediatric SAE and compares patients with and without formal neuropsychological assessments to determine factors influencing cognitive impairment. Methods: A retrospective review was conducted on 155 pediatric autoimmune encephalitis cases, including 80 with SAE. Eleven had neuropsychological evaluations. Statistical analyses assessed differences in age, disease severity, lesion characteristics, hospitalization, and treatment needs. Results: Executive dysfunction was present in 75% of SAE cases. Patients with neuropsychological evaluations were older (median: 8 vs. 3 years, p = 0.0115) and had more severe encephalitis at admission (p = 0.0391) and one year later (p = 0.0011). Lesion burden did not differ (p > 0.05), but patients with assessments had longer hospitalizations and required more intensive treatments (p < 0.005). Conclusions: Executive dysfunction in pediatric SAE is linked to disease severity rather than lesion burden. Systematic neuropsychological assessments should be integrated into patient care. Deeper phenotyping of cognitive profiles and identifying risk factors for poor prognosis will help personalize care in order to improve outcomes.