Stroke ranks among the top 10 most common causes of death in children. Recently, there has been a significant increase in the number of strokes in the pediatric population. Mechanical thrombectomy is an uncommon method for treating acute ischemic stroke (AIS) in children. This case report discusses a 13-year-old girl with a history of ischemic stroke for the past 3 months, obesity, hypertension, and antiphospholipid syndrome (APS, treated with rivaroxaban), who suffered another ischemic stroke and underwent mechanical thrombectomy with favorable clinical outcomes. Additionally, the patient was diagnosed with antithrombin III deficiency. It is necessary to identify risk factors for AIS in the pediatric population, such as thrombophilia or autoimmune diseases, such as antiphospholipid syndrome, and to develop guidelines for the use of thrombectomy in children. This method could reduce mortality, improve quality of life, prevent disability, and lower future medical costs.