BACKGROUND Hemoglobin Hornchurch is regarded as an asymptomatic hemoglobinopathy with no obvious hematological or clinical abnormalities. Recently, we identified hemoglobin Hornchurch in a 13-year-old Chinese boy complicated with thrombocytopenia, which displayed instability in isopropanol precipitation test. METHODS In this case report, we reported a Chinese boy with hemoglobin Hornchurch complicated by thrombocytopenia. The patients have been misdiagnosed as aplastic anemia and myelodysplastic syndrome before. METHODS Hemolysis tests, high-performance liquid chromatography, and HBB gene sequencing identified the E44K (G>A) mutation. Isopropanol precipitation test showed instability in hemoglobin Hornchurch. METHODS The patient was given immunosuppressive therapy for 3 months. RESULTS His general conditions have improved along with the recovery of the hemogram index. CONCLUSIONS Further research is needed to clarify the relation between structural abnormality and functional properties of hemoglobin Hornchurch. This second case of hemoglobin Hornchurch indicates that there might be more hemoglobin variants or their carriers in the Chinese population.