Introduction: In childhood, thrombocytopenia caused by transient antibody-mediated thrombocyte destruction is most frequently diagnosed as immune thrombocytopenic purpura (ITP). We report the case of a girl with ITP associated with autoimmune thyroiditis. Case presentation: A 11-year-old female patient with Hashimoto’s thyroiditis presented with clinical signs of petechiae and ecchymoses on the extremities. Laboratory tests showed remarkable thrombocytopenia with a platelet count of 44,500/μL, hence she was referred to a hematologic consultation. The peripheral blood smear showed normal size platelets in very low range. The bone marrow examination exposed hyperplasia of the megakaryocyte series with outwardly morphologic abnormalities. The patient was diagnosed with ITP, and her first-line treatment was pulsed steroid and immunoglobulin therapy. The thrombocytopenia was refractory to these first-line medications. After 6 months of corticotherapy and a period of severe menorrhagia, azathioprine immunosupression was initiated as a second-line treatment. Her platelet count rapidly increased, and the evolution was good, without bleeding complications. Conclusion: In case of a medical history of autoimmune diseases and treatment-resistant ITP, attention must be focused on detecting coexisting autoimmune diseases and adjusting the treatment in accordance with the chronic evolution of the disease.