Non-Hodgkin lymphoma can disseminate to the central nervous system at initiation of treatment for systemic lymphoma or spread during the relapse of systematic lymphoma with CNS involvement, which is defined as secondary central nervous system lymphoma (SCNSL). The incidence of SCNSL depends on the pathological type of lymphoma and is especially high in aggressive lymphoma. SCNSL has a poor prognosis because of the lack of effective treatment regimens. This article presents a rare case of SCNSL; an individualized treatment regimen was designed according to the genetic analyses of the patient tumor and included a Bruton's tyrosine kinase (BTK) inhibitor. After six cycles of treatment and another two cycles of rituximab, most lesions lost their metabolic activity. However, in the final stage of treatment, our patient unfortunately suffered from respiratory failure, which revealed that we should pay attention to Pneumocystis jirovecii pneumonia during ibrutinib treatment.