Introduction: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused the enduring global COVID-19 pandemic, which has already begun in late 2019. The virus affects various organs, including the nervous system. This study investigates neurological complications in children with COVID-19 or multisystem inflammatory syndrome in children (MIS-C) in the South Moravia region (Czech republic), where a high COVID-19 rate among children (35.790/100.000) allows for a comprehensive analysis. Methods: Data from the University Hospital Brno (from March 2020 to February 2022) were analyzed to study two groups of hospitalized children diagnosed with COVID-19 or MIS-C: one experiencing neurological complications, and the other without neurological symptoms. The analysis included demographics, admission reasons, infection severity and progression, objective neurological findings, hospitalization details, MIS-C presence and therapies used. Descriptive statistics and statistical testing were employed to assess how individual factors influenced neurological complication rates within these groups. Results: Among 420 hospitalized children with COVID-19 or MIS-C, 26 (6.2%) had neurological complications. Preexisting neurological deficits increased the likelihood of worse outcomes (P = 0.0224). Significant differences in hospitalization length (P = 0.0012), infection severity (P = 0.0052), and outcome (P < 0.0001) occurred between groups. Conclusion: Continuous monitoring and further research on neurological complications in children with COVID-19 or MIS-C are crucial for better understanding of the course of the disease and minimize complications after infection.