Background <p>Ataxia-telangiectasia (A-T) is an infrequent autosomal recessive multisystemic disorder caused by <i>ATM</i> variants. It is characterized by progressive cerebellar ataxia, telangiectasia, susceptibility to malignancies and variable immunodeficiency. Patients have phenotypic heterogeneity, especially those with variant A-T form, posing challenges for early diagnosis and intervention.</p> Case presentation <p>Herein we describe an early-onset A-T patient with atypical symptoms, mainly manifested as immunodeficiency and isolated intractable thrombocytopenia, which led to the initial suspicion of immune thrombocytopenia. The patient did not receive a definitive diagnosis of variant A-T until genetic testing was performed and detected a compound heterozygous genotype in <i>ATM</i>. Anti-infective therapy, intravenous immunoglobulin, methylprednisolone as well as treatment of thrombopoietin were administered. The infection was controlled, but therapies had limited effect on the thrombocytopenia. Finally, patient was discharged voluntarily after 17 days of hospitalization with a last platelet count of 29 × 10⁹/L.</p> Conclusions <p>This case suggests that A-T should be considered among children with recurrent infections, immunodeficiency and/or thrombocytopenia, even in the absence of typical symptoms, for the sake of reducing incorrect or missed diagnosis. Genetic testing is an efficient tool for early identification and intervention. This report details the phenotype and management of secondary thrombocytopenia in A-T, enhancing clinicians’ insights into the disorder.</p>