Introduction: Methimazole is considered the first-line antithyroid drug for Graves’ disease (GD) in children and adolescents. However, it can lead to severe adverse effects, such as agranulocytosis, which can result from direct drug toxicity or immune-mediated responses. This report aims to describe the clinical management of an adolescent with GD who developed agranulocytosis following methimazole administration. Case Presentation: A 13-year-old female, diagnosed with GD, developed neutropenia six months after starting methimazole. She was admitted with high-grade fever, sore throat, palpitations, fatigue, myalgia, and diarrhea. The treatment regimen included filgrastim, antibiotics, β-blockers, a solution of potassium iodide (SSKI), cholestyramine, and lithium. Within seven days, her absolute neutrophil count gradually improved, her fever subsided, her hyperthyroidism was controlled, and she was discharged. Discussion: Antithyroid drug-induced neutropenia represents a serious complication. In these patients, effective infection management, control of hyperthyroidism, and supportive measures to promptly increase the neutrophil count can reduce the associated morbidity and mortality. Conclusions: Close monitoring and awareness of risk factors, such as age, female sex, and higher doses of methimazole, may decrease the risk of agranulocytosis and its fatal outcomes. Alternative treatments to control hyperthyroidism during methimazole-induced agranulocytosis include β-blockade, potassium iodide solution (SSKI), cholestyramine, steroids, and lithium.