Zika virus (ZIKV) is a mosquito-borne viral infection that is shed in biological fluids promoting vertical and sexual transmission. Recent outbreaks of ZIKV have been associated with an increase in adult and fetal infection-related diseases. ZIKV infection in rhesus macaques is considered a robust animal model for studying Zika viral infection dynamics and fetal disease. A compelling feature of ZIKV is its ability to persist for long periods of time in immunocompetent hosts and during pregnancy, which may be linked to adverse infection outcomes. One consistent site of viral persistence is lymph node tissues. Utilizing this feature of ZIKV infection could be useful to diagnose viral persistence and to improve efficacy evaluation of antiviral vaccines and therapeutics, as well as for diagnostic and prognostic assessments in humans. We have developed a protocol to isolate lymph node cells using cell type-specific antibody-magnetic bead techniques followed by a one-step qRT-PCR detection of Zika virus RNA. This method fostered the identification of dendritic cells, macrophages, and B cells from the lymph node and spleen as harboring persistent ZIKV RNA.