Diagnosis of a second HIV-associated non-Hodgkin lymphoma (HIV-NHL) is rare, but additional cases may occur as aggressive therapy for both HIV and NHL improves. An 11-year-old presented with a second primary HIV-NHL following remission for 9 years. Analysis of the tumor demonstrated presence of EBV and HIV with absence of CMV, HHV-8, and HHV-6. Although microscopic disease was present only in CSF, analysis of peripheral blood and bone marrow by PCR was positive. The patient underwent a stem cell transplant, but within 3 months, his disease recurred. Analysis for residual disease and viruses in similar cases may provide information in understanding pediatric HIV-NHL.