In this case report, we report a pediatric patient with COVID-19 and atypical hemolytic uremic syndrome (aHUS). A 3-year-old girl with fever and respiratory distress was admitted to the hospital. The patient tested positive for COVID-19 by a PCR test. As her respiratory distress increased and blood gas indicated deep respiratory acidosis on the third day of the pediatric intensive care unit follow-up, the patient was intubated and ventilated. Thorax computerized tomography (CT) showed bilateral effusion and atelectasis. During her follow-up, the pleural effusion resolved but there were marked consolidation areas and ground glass opacities compatible with COVID-19 on the follow-up CT. On the 10th day, she became anuric and developed progressive thrombocytopenia and persistent microangiopathic hemolytic anemia, which were suggestive of HUS given a high creatinine level (1.9 mg/dl), an undetectable haptoglobin level, reticulocytosis (8%), and an LDH level of 2540 U/l. Direct Coombs test returned negative. Examination of a peripheral blood smear revealed schistocytes. Disseminated intravascular coagulation was ruled out by normal INR and PTT. In the light of the available findings, we considered the patient to have thrombotic microangiopathy (TMA) triggered by COVID-19. It was not a TTP-form of TMA but rather an aHUS type, based on an ADAMTS13 activity level >5%. Hence, plasmapheresis was performed with fresh frozen plasma (FFP). After 4 weeks, she became completely asymptomatic, and her hemodynamic parameters normalized. COVID-19 induced uncontrolled complement activation leading to the development of aHUS. Early diagnosis and treatment may reduce morbidity and mortality since its treatment options.