Background: The COVID-19 pandemic, caused by the novel SARS-CoV-2 virus, has presented significant challenges to global healthcare systems, affecting individuals of all ages, including neonates. Recent studies have identified a condition similar to Multisystem Inflammatory Syndrome in Children (MIS-C) occurring in neonates, termed MIS-N (Multisystem Inflammatory Syndrome in Neonates), linked to maternal infection with SARS-CoV-2. Understanding MIS-N's clinical manifestations, laboratory findings, and treatment outcomes is crucial for improving neonatal care during the ongoing pandemic. Objective: The objective of this study was to explore the clinical characteristics, laboratory diagnostics, and treatment outcomes of neonates diagnosed with MIS-N, aiming to contribute to better diagnostic and management approaches for this vulnerable population. Methods: This retrospective case series analyzed neonates admitted with suspected MIS-N to the Children's Medical Center in Tehran, Iran, from March to September 2020. Inclusion criteria encompassed neonates showing clinical signs suggestive of MIS-N, elevated inflammatory markers, and positive for SARS-CoV-2 antibodies. Key data points included demographic information, clinical presentation, laboratory results (including complete blood count, inflammatory markers, and specific COVID-19 serology), treatment modalities, and patient outcomes. The effectiveness of interventions was evaluated based on symptom resolution and normalization of lab values. Results: Two neonates were identified with MIS-N. Case I involved a 39-week-old male presenting with diarrhea, dehydration, fever, and a rash, with initial inflammatory markers showing a white blood count (WBC) of 23,000 cells/μL, C-reactive protein (CRP) of 93 mg/L, and serum IgG of 10 g/L. Following treatment with corticosteroids, the patient's condition stabilized, with a decrease in WBC to 18,000 cells/μL and CRP to 34 mg/L. Case II, a 38-week-old female, exhibited a cough, rashes, with WBC of 17,000 cells/μL, CRP of 2 mg/L, and serum IgG of 40 g/L. A single dose of hydrocortisone led to symptom resolution. Both cases had no significant adverse outcomes at a three-month follow-up. Conclusion: Our findings illuminate the clinical and laboratory characteristics of MIS-N in neonates, emphasizing the role of maternal SARS-CoV-2 infection in its etiology. The successful resolution of symptoms with corticosteroid treatment highlights the potential efficacy of this intervention in managing MIS-N. These insights contribute to the growing understanding of MIS-N and underscore the need for ongoing research to define optimal diagnostic criteria and treatment protocols.