Isolated central nervous system (CNS) relapse of non-Hodgkin lymphoma (NHL) is very rare. We report a five-year-old boy with T-cell lymphoblastic lymphoma (T-LBL), who developed CNS relapse under treatment when the primary tumor was in complete remission. The patient presented initially with persistent cough and an anterior mediastinal mass and had no bone marrow or CNS involvement at diagnosis. During re-induction treatment, a routine lumbar puncture revealed blasts in the cerebrospinal fluid (CSF). The patient developed neurological signs and symptoms consequently. Craniospinal radiotherapy followed by BFM (Berlin-Frankfurt-Munster) high-risk chemotherapy protocol was initiated. Despite complete response after three courses, the patient experienced CNS relapse and expired due to disease progression. In the treatment of a NHL patient, routine CSF analysis should be done for tumor cells even when the primary disease is in complete remission.