Introduction: the new coronavirus pandemic has been a reality throughout 2020, and it has brought great challenges. The virus predominantly manifests in the pediatric population with mild symptoms. However, an increase in the incidence of Multisystemic Inflammatory Syndrome in Children (MIS-C) associated with COVID-19 has been described in the literature. MIS-C manifests mainly with fever and gastrointestinal symptoms and may mimic acute abdomen due to acute appendicitis. The objective of this study is to propose a care flowchart for suspected cases of acute appendicitis in the initial phase in pandemic times, considering the possibility of MIS-C. This situation was brought up by a patient treated in a pediatric hospital in Brazil. Discussion: It was possible to identify common signs and symptoms in the reported patient and those published cases that may serve as alerts for early identification of MIS-C cases. Based on the literature review and on the similarities between the syndrome and the inflammatory acute abdomen in children, we elaborated an initial approach for these cases to facilitate the identification, early diagnosis, and management. The flowchart considers details of the clinical history, physical examination, and complementary exams prior to the indication of appendectomy in patients with initial phase symptoms. Conclusion: MIS-C, although rare and of poorly known pathophysiology, is most often severe and has a high mortality risk. The use of the proposed flowchart can help in the diagnosis and early treatment of MIS-C.